R Basics

Introduction

To enter code use command+enter

R Calculator

Basic calculations:

1+100
[1] 101
2^2
[1] 4
7/2
[1] 3.5
10-2
[1] 8
2*2
[1] 4

Order of operations matter: PEMDAS

3+5*2
[1] 13
(3+5)*2
[1] 16

Using scientific notation:

2e2
[1] 200
2/10000
[1] 2e-04

Can also use trigometric functions:

log(1)
[1] 0
exp(0)
[1] 1

You can also ask questions: T/F Statements

1 == 1
[1] TRUE
1 >=1
[1] TRUE
1 < 1
[1] FALSE
1 != 2
[1] TRUE

You can define objects/variables:

x <- 10
x
[1] 10
x+x
[1] 20
y <- x+x
y
[1] 20

Vectorization

Use the colon : to make a list:

1:5
[1] 1 2 3 4 5

Conducting operations on vectors:

2^(1:5)
[1]  2  4  8 16 32

Storing vector as an object:

v <- 1:5
2^v
[1]  2  4  8 16 32

Log transformations:

log10(v)
[1] 0.0000000 0.3010300 0.4771213 0.6020600 0.6989700

Environment

To see what is in current environment us ls() command:

ls()
 [1] "ab"                    "AfricanLifeExpectancy" "Africas"               "another_list"          "avg.rand"             
 [6] "beer"                  "cats"                  "cor.gen"               "df_example"            "exp"                  
[11] "f"                     "f2"                    "forestdata"            "g"                     "gapminder"            
[16] "gapminder2"            "gen.reg"               "gp"                    "habitat.t2"            "habitat.tgreater"     
[21] "habitat.tless"         "kigweught"             "list_example"          "log.left.bulb"         "logweight"            
[26] "m"                     "matrix_example"        "n"                     "obs"                   "obs_fair"             
[31] "obs_weighted"          "p"                     "peds"                  "penguin_pca"           "penguins"             
[36] "penguins_matrix"       "penguins_raw"          "penguins2"             "rand"                  "spearman.cor.gen"     
[41] "spid.gen"              "v"                     "x"                     "xlist"                 "y"                    
[46] "z"                    

To remove items from environment, use rm() command:

rm(x)
ls()
 [1] "ab"                    "AfricanLifeExpectancy" "Africas"               "another_list"          "avg.rand"             
 [6] "beer"                  "cats"                  "cor.gen"               "df_example"            "exp"                  
[11] "f"                     "f2"                    "forestdata"            "g"                     "gapminder"            
[16] "gapminder2"            "gen.reg"               "gp"                    "habitat.t2"            "habitat.tgreater"     
[21] "habitat.tless"         "kigweught"             "list_example"          "log.left.bulb"         "logweight"            
[26] "m"                     "matrix_example"        "n"                     "obs"                   "obs_fair"             
[31] "obs_weighted"          "p"                     "peds"                  "penguin_pca"           "penguins"             
[36] "penguins_matrix"       "penguins_raw"          "penguins2"             "rand"                  "spearman.cor.gen"     
[41] "spid.gen"              "v"                     "xlist"                 "y"                     "z"                    

Package Management

To see what is already present, use command:

installed.packages()
                     Package                LibPath                                                          Version     
ade4                 "ade4"                 "/Library/Frameworks/R.framework/Versions/4.2/Resources/library" "1.7-19"    
ambient              "ambient"              "/Library/Frameworks/R.framework/Versions/4.2/Resources/library" "1.0.2"     
AnnotationDbi        "AnnotationDbi"        "/Library/Frameworks/R.framework/Versions/4.2/Resources/library" "1.58.0"    
ape                  "ape"                  "/Library/Frameworks/R.framework/Versions/4.2/Resources/library" "5.6-2"     
aplot                "aplot"                "/Library/Frameworks/R.framework/Versions/4.2/Resources/library" "0.1.8"     
askpass              "askpass"              "/Library/Frameworks/R.framework/Versions/4.2/Resources/library" "1.1"       
assertthat           "assertthat"           "/Library/Frameworks/R.framework/Versions/4.2/Resources/library" "0.2.1"     
backports            "backports"            "/Library/Frameworks/R.framework/Versions/4.2/Resources/library" "1.4.1"     
base                 "base"                 "/Library/Frameworks/R.framework/Versions/4.2/Resources/library" "4.2.1"     
base64enc            "base64enc"            "/Library/Frameworks/R.framework/Versions/4.2/Resources/library" "0.1-3"     
BayesFactor          "BayesFactor"          "/Library/Frameworks/R.framework/Versions/4.2/Resources/library" "0.9.12-4.4"
bayesm               "bayesm"               "/Library/Frameworks/R.framework/Versions/4.2/Resources/library" "3.1-4"     
bayestestR           "bayestestR"           "/Library/Frameworks/R.framework/Versions/4.2/Resources/library" "0.13.0"    
BH                   "BH"                   "/Library/Frameworks/R.framework/Versions/4.2/Resources/library" "1.78.0-0"  
Biobase              "Biobase"              "/Library/Frameworks/R.framework/Versions/4.2/Resources/library" "2.56.0"    
BiocFileCache        "BiocFileCache"        "/Library/Frameworks/R.framework/Versions/4.2/Resources/library" "2.4.0"     
BiocGenerics         "BiocGenerics"         "/Library/Frameworks/R.framework/Versions/4.2/Resources/library" "0.42.0"    
BiocIO               "BiocIO"               "/Library/Frameworks/R.framework/Versions/4.2/Resources/library" "1.6.0"     
BiocManager          "BiocManager"          "/Library/Frameworks/R.framework/Versions/4.2/Resources/library" "1.30.18"   
BiocParallel         "BiocParallel"         "/Library/Frameworks/R.framework/Versions/4.2/Resources/library" "1.30.4"    
BiocVersion          "BiocVersion"          "/Library/Frameworks/R.framework/Versions/4.2/Resources/library" "3.15.2"    
biomaRt              "biomaRt"              "/Library/Frameworks/R.framework/Versions/4.2/Resources/library" "2.52.0"    
biomformat           "biomformat"           "/Library/Frameworks/R.framework/Versions/4.2/Resources/library" "1.24.0"    
Biostrings           "Biostrings"           "/Library/Frameworks/R.framework/Versions/4.2/Resources/library" "2.64.1"    
bit                  "bit"                  "/Library/Frameworks/R.framework/Versions/4.2/Resources/library" "4.0.4"     
bit64                "bit64"                "/Library/Frameworks/R.framework/Versions/4.2/Resources/library" "4.0.5"     
bitops               "bitops"               "/Library/Frameworks/R.framework/Versions/4.2/Resources/library" "1.0-7"     
blob                 "blob"                 "/Library/Frameworks/R.framework/Versions/4.2/Resources/library" "1.2.3"     
boot                 "boot"                 "/Library/Frameworks/R.framework/Versions/4.2/Resources/library" "1.3-28"    
brew                 "brew"                 "/Library/Frameworks/R.framework/Versions/4.2/Resources/library" "1.0-8"     
brio                 "brio"                 "/Library/Frameworks/R.framework/Versions/4.2/Resources/library" "1.1.3"     
broom                "broom"                "/Library/Frameworks/R.framework/Versions/4.2/Resources/library" "1.0.1"     
bslib                "bslib"                "/Library/Frameworks/R.framework/Versions/4.2/Resources/library" "0.4.0"     
cachem               "cachem"               "/Library/Frameworks/R.framework/Versions/4.2/Resources/library" "1.0.6"     
callr                "callr"                "/Library/Frameworks/R.framework/Versions/4.2/Resources/library" "3.7.2"     
cellranger           "cellranger"           "/Library/Frameworks/R.framework/Versions/4.2/Resources/library" "1.1.0"     
class                "class"                "/Library/Frameworks/R.framework/Versions/4.2/Resources/library" "7.3-20"    
classInt             "classInt"             "/Library/Frameworks/R.framework/Versions/4.2/Resources/library" "0.4-8"     
cli                  "cli"                  "/Library/Frameworks/R.framework/Versions/4.2/Resources/library" "3.4.1"     
clipr                "clipr"                "/Library/Frameworks/R.framework/Versions/4.2/Resources/library" "0.8.0"     
cluster              "cluster"              "/Library/Frameworks/R.framework/Versions/4.2/Resources/library" "2.1.4"     
coda                 "coda"                 "/Library/Frameworks/R.framework/Versions/4.2/Resources/library" "0.19-4"    
codetools            "codetools"            "/Library/Frameworks/R.framework/Versions/4.2/Resources/library" "0.2-18"    
colorspace           "colorspace"           "/Library/Frameworks/R.framework/Versions/4.2/Resources/library" "2.0-3"     
commonmark           "commonmark"           "/Library/Frameworks/R.framework/Versions/4.2/Resources/library" "1.8.1"     
compiler             "compiler"             "/Library/Frameworks/R.framework/Versions/4.2/Resources/library" "4.2.1"     
compositions         "compositions"         "/Library/Frameworks/R.framework/Versions/4.2/Resources/library" "2.0-4"     
contfrac             "contfrac"             "/Library/Frameworks/R.framework/Versions/4.2/Resources/library" "1.1-12"    
correlation          "correlation"          "/Library/Frameworks/R.framework/Versions/4.2/Resources/library" "0.8.3"     
cpp11                "cpp11"                "/Library/Frameworks/R.framework/Versions/4.2/Resources/library" "0.4.3"     
crayon               "crayon"               "/Library/Frameworks/R.framework/Versions/4.2/Resources/library" "1.5.2"     
credentials          "credentials"          "/Library/Frameworks/R.framework/Versions/4.2/Resources/library" "1.3.2"     
curl                 "curl"                 "/Library/Frameworks/R.framework/Versions/4.2/Resources/library" "4.3.3"     
dada2                "dada2"                "/Library/Frameworks/R.framework/Versions/4.2/Resources/library" "1.24.0"    
data.table           "data.table"           "/Library/Frameworks/R.framework/Versions/4.2/Resources/library" "1.14.4"    
datasets             "datasets"             "/Library/Frameworks/R.framework/Versions/4.2/Resources/library" "4.2.1"     
datawizard           "datawizard"           "/Library/Frameworks/R.framework/Versions/4.2/Resources/library" "0.6.3"     
DBI                  "DBI"                  "/Library/Frameworks/R.framework/Versions/4.2/Resources/library" "1.1.3"     
dbplyr               "dbplyr"               "/Library/Frameworks/R.framework/Versions/4.2/Resources/library" "2.2.1"     
DECIPHER             "DECIPHER"             "/Library/Frameworks/R.framework/Versions/4.2/Resources/library" "2.24.0"    
DelayedArray         "DelayedArray"         "/Library/Frameworks/R.framework/Versions/4.2/Resources/library" "0.22.0"    
deldir               "deldir"               "/Library/Frameworks/R.framework/Versions/4.2/Resources/library" "1.0-6"     
                     Priority     
ade4                 NA           
ambient              NA           
AnnotationDbi        NA           
ape                  NA           
aplot                NA           
askpass              NA           
assertthat           NA           
backports            NA           
base                 "base"       
base64enc            NA           
BayesFactor          NA           
bayesm               NA           
bayestestR           NA           
BH                   NA           
Biobase              NA           
BiocFileCache        NA           
BiocGenerics         NA           
BiocIO               NA           
BiocManager          NA           
BiocParallel         NA           
BiocVersion          NA           
biomaRt              NA           
biomformat           NA           
Biostrings           NA           
bit                  NA           
bit64                NA           
bitops               NA           
blob                 NA           
boot                 "recommended"
brew                 NA           
brio                 NA           
broom                NA           
bslib                NA           
cachem               NA           
callr                NA           
cellranger           NA           
class                "recommended"
classInt             NA           
cli                  NA           
clipr                NA           
cluster              "recommended"
coda                 NA           
codetools            "recommended"
colorspace           NA           
commonmark           NA           
compiler             "base"       
compositions         NA           
contfrac             NA           
correlation          NA           
cpp11                NA           
crayon               NA           
credentials          NA           
curl                 NA           
dada2                NA           
data.table           NA           
datasets             "base"       
datawizard           NA           
DBI                  NA           
dbplyr               NA           
DECIPHER             NA           
DelayedArray         NA           
deldir               NA           
                     Depends                                                                                                                                                                                                                                
ade4                 "R (>= 2.10)"                                                                                                                                                                                                                          
ambient              "R (>= 3.0.2)"                                                                                                                                                                                                                         
AnnotationDbi        "R (>= 2.7.0), methods, utils, stats4, BiocGenerics (>=\n0.29.2), Biobase (>= 1.17.0), IRanges"                                                                                                                                        
ape                  "R (>= 3.2.0)"                                                                                                                                                                                                                         
aplot                NA                                                                                                                                                                                                                                     
askpass              NA                                                                                                                                                                                                                                     
assertthat           NA                                                                                                                                                                                                                                     
backports            "R (>= 3.0.0)"                                                                                                                                                                                                                         
base                 NA                                                                                                                                                                                                                                     
base64enc            "R (>= 2.9.0)"                                                                                                                                                                                                                         
BayesFactor          "R (>= 3.2.0), coda, Matrix (>= 1.1-1)"                                                                                                                                                                                                
bayesm               "R (>= 3.2.0)"                                                                                                                                                                                                                         
bayestestR           "R (>= 3.6)"                                                                                                                                                                                                                           
BH                   NA                                                                                                                                                                                                                                     
Biobase              "R (>= 2.10), BiocGenerics (>= 0.27.1), utils"                                                                                                                                                                                         
BiocFileCache        "R (>= 3.4.0), dbplyr (>= 1.0.0)"                                                                                                                                                                                                      
BiocGenerics         "R (>= 4.0.0), methods, utils, graphics, stats"                                                                                                                                                                                        
BiocIO               "R (>= 4.0)"                                                                                                                                                                                                                           
BiocManager          NA                                                                                                                                                                                                                                     
BiocParallel         "methods, R (>= 3.5.0)"                                                                                                                                                                                                                
BiocVersion          "R (>= 4.2.0)"                                                                                                                                                                                                                         
biomaRt              "methods"                                                                                                                                                                                                                              
biomformat           "R (>= 3.2), methods"                                                                                                                                                                                                                  
Biostrings           "R (>= 4.0.0), methods, BiocGenerics (>= 0.37.0), S4Vectors (>=\n0.27.12), IRanges (>= 2.30.1), XVector (>= 0.29.2),\nGenomeInfoDb"                                                                                                    
bit                  "R (>= 2.9.2)"                                                                                                                                                                                                                         
bit64                "R (>= 3.0.1), bit (>= 4.0.0), utils, methods, stats"                                                                                                                                                                                  
bitops               NA                                                                                                                                                                                                                                     
blob                 NA                                                                                                                                                                                                                                     
boot                 "R (>= 3.0.0), graphics, stats"                                                                                                                                                                                                        
brew                 NA                                                                                                                                                                                                                                     
brio                 NA                                                                                                                                                                                                                                     
broom                "R (>= 3.1)"                                                                                                                                                                                                                           
bslib                "R (>= 2.10)"                                                                                                                                                                                                                          
cachem               NA                                                                                                                                                                                                                                     
callr                "R (>= 3.4)"                                                                                                                                                                                                                           
cellranger           "R (>= 3.0.0)"                                                                                                                                                                                                                         
class                "R (>= 3.0.0), stats, utils"                                                                                                                                                                                                           
classInt             "R (>= 2.2)"                                                                                                                                                                                                                           
cli                  "R (>= 3.4)"                                                                                                                                                                                                                           
clipr                NA                                                                                                                                                                                                                                     
cluster              "R (>= 3.5.0)"                                                                                                                                                                                                                         
coda                 "R (>= 2.14.0)"                                                                                                                                                                                                                        
codetools            "R (>= 2.1)"                                                                                                                                                                                                                           
colorspace           "R (>= 3.0.0), methods"                                                                                                                                                                                                                
commonmark           NA                                                                                                                                                                                                                                     
compiler             NA                                                                                                                                                                                                                                     
compositions         "R (>= 3.6)"                                                                                                                                                                                                                           
contfrac             NA                                                                                                                                                                                                                                     
correlation          "R (>= 3.6)"                                                                                                                                                                                                                           
cpp11                NA                                                                                                                                                                                                                                     
crayon               NA                                                                                                                                                                                                                                     
credentials          NA                                                                                                                                                                                                                                     
curl                 "R (>= 3.0.0)"                                                                                                                                                                                                                         
dada2                "R (>= 3.4.0), Rcpp (>= 0.12.0), methods (>= 3.4.0)"                                                                                                                                                                                   
data.table           "R (>= 3.1.0)"                                                                                                                                                                                                                         
datasets             NA                                                                                                                                                                                                                                     
datawizard           "R (>= 3.6)"                                                                                                                                                                                                                           
DBI                  "methods, R (>= 3.0.0)"                                                                                                                                                                                                                
dbplyr               "R (>= 3.1)"                                                                                                                                                                                                                           
DECIPHER             "R (>= 3.5.0), Biostrings (>= 2.59.1), RSQLite (>= 1.1), stats,\nparallel"                                                                                                                                                             
DelayedArray         "R (>= 4.0.0), methods, stats4, Matrix, BiocGenerics (>=\n0.37.0), MatrixGenerics (>= 1.1.3), S4Vectors (>= 0.27.2),\nIRanges (>= 2.17.3)"                                                                                             
deldir               "R (>= 3.5.0)"                                                                                                                                                                                                                         
                     Imports                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
ade4                 "graphics, grDevices, methods, stats, utils, MASS, pixmap, sp"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
ambient              "rlang, grDevices, graphics, stats"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
AnnotationDbi        "DBI, RSQLite, S4Vectors (>= 0.9.25), stats, KEGGREST"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
ape                  "nlme, lattice, graphics, methods, stats, tools, utils,\nparallel, Rcpp (>= 0.12.0)"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
aplot                "ggfun (>= 0.0.6), ggplot2, ggplotify, patchwork, magrittr,\nmethods, utils"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
askpass              "sys (>= 2.1)"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
assertthat           "tools"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
backports            NA                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
base                 NA                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
base64enc            NA                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
BayesFactor          "pbapply, mvtnorm, stringr, utils, graphics, MatrixModels, Rcpp\n(>= 0.11.2), methods, hypergeo"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
bayesm               "Rcpp (>= 0.12.0), utils, stats, graphics, grDevices"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
bayestestR           "insight (>= 0.18.2), datawizard (>= 0.5.1), graphics, methods,\nstats, utils"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
BH                   NA                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
Biobase              "methods"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
BiocFileCache        "methods, stats, utils, dplyr, RSQLite, DBI, rappdirs,\nfilelock, curl, httr"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
BiocGenerics         "methods, utils, graphics, stats"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
BiocIO               "BiocGenerics, S4Vectors, methods, tools"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
BiocManager          "utils"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
BiocParallel         "stats, utils, futile.logger, parallel, snow, codetools"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
BiocVersion          NA                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
biomaRt              "utils, XML (>= 3.99-0.7), AnnotationDbi, progress, stringr,\nhttr, digest, BiocFileCache, rappdirs, xml2"                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
biomformat           "plyr (>= 1.8), jsonlite (>= 0.9.16), Matrix (>= 1.2), rhdf5"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
Biostrings           "methods, utils, grDevices, graphics, stats, crayon"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
bit                  NA                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
bit64                NA                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
bitops               NA                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
blob                 "methods, rlang, vctrs (>= 0.2.1)"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
boot                 NA                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
brew                 NA                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
brio                 NA                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
broom                "backports, dplyr (>= 1.0.0), ellipsis, generics (>= 0.0.2),\nglue, purrr, rlang, stringr, tibble (>= 3.0.0), tidyr (>=\n1.0.0), ggplot2"                                                                                                                                                                                                                                                                                                                                                                                                                                                
bslib                "grDevices, htmltools (>= 0.5.2), jsonlite, sass (>= 0.4.0),\njquerylib (>= 0.1.3), rlang, cachem, memoise"                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
cachem               "rlang, fastmap"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
callr                "processx (>= 3.6.1), R6, utils"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
cellranger           "rematch, tibble"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
class                "MASS"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
classInt             "grDevices, stats, graphics, e1071, class, KernSmooth"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
cli                  "utils"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
clipr                "utils"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
cluster              "graphics, grDevices, stats, utils"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
coda                 "lattice"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
codetools            NA                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
colorspace           "graphics, grDevices, stats"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
commonmark           NA                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
compiler             NA                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
compositions         "methods, utils, grDevices, stats, tensorA, robustbase, bayesm,\ngraphics, MASS"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
contfrac             NA                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
correlation          "bayestestR (>= 0.13.0), datasets, datawizard (>= 0.5.1),\ninsight (>= 0.18.4), parameters (>= 0.18.2), stats"                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
cpp11                NA                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
crayon               "grDevices, methods, utils"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
credentials          "openssl (>= 1.3), sys (>= 2.1), curl, jsonlite, askpass"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
curl                 NA                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
dada2                "Biostrings (>= 2.42.1), ggplot2 (>= 2.1.0), reshape2 (>=\n1.4.1), ShortRead (>= 1.32.0), RcppParallel (>= 4.3.0),\nparallel (>= 3.2.0), IRanges (>= 2.6.0), XVector (>= 0.16.0),\nBiocGenerics (>= 0.22.0)"                                                                                                                                                                                                                                                                                                                                                                             
data.table           "methods"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
datasets             NA                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
datawizard           "insight (>= 0.18.5), stats, utils"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
DBI                  NA                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
dbplyr               "assertthat (>= 0.2.0), blob (>= 1.2.0), cli (>= 3.3.0), DBI\n(>= 1.0.0), dplyr (>= 1.0.9), glue (>= 1.2.0), lifecycle (>=\n1.0.0), magrittr, methods, pillar (>= 1.5.0), purrr (>= 0.2.5),\nR6 (>= 2.2.2), rlang (>= 1.0.0), tibble (>= 1.4.2), tidyselect\n(>= 0.2.4), utils, vctrs (>= 0.4.1), withr"                                                                                                                                                                                                                                                                                 
DECIPHER             "methods, DBI, S4Vectors, IRanges, XVector"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
DelayedArray         "stats"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
deldir               "graphics, grDevices"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
                     LinkingTo                                                     
ade4                 NA                                                            
ambient              "cpp11 (>= 0.4.2)"                                            
AnnotationDbi        NA                                                            
ape                  "Rcpp"                                                        
aplot                NA                                                            
askpass              NA                                                            
assertthat           NA                                                            
backports            NA                                                            
base                 NA                                                            
base64enc            NA                                                            
BayesFactor          "Rcpp (>= 0.11.2), RcppEigen (>= 0.3.2.2.0)"                  
bayesm               "Rcpp, RcppArmadillo"                                         
bayestestR           NA                                                            
BH                   NA                                                            
Biobase              NA                                                            
BiocFileCache        NA                                                            
BiocGenerics         NA                                                            
BiocIO               NA                                                            
BiocManager          NA                                                            
BiocParallel         "BH"                                                          
BiocVersion          NA                                                            
biomaRt              NA                                                            
biomformat           NA                                                            
Biostrings           "S4Vectors, IRanges, XVector"                                 
bit                  NA                                                            
bit64                NA                                                            
bitops               NA                                                            
blob                 NA                                                            
boot                 NA                                                            
brew                 NA                                                            
brio                 NA                                                            
broom                NA                                                            
bslib                NA                                                            
cachem               NA                                                            
callr                NA                                                            
cellranger           NA                                                            
class                NA                                                            
classInt             NA                                                            
cli                  NA                                                            
clipr                NA                                                            
cluster              NA                                                            
coda                 NA                                                            
codetools            NA                                                            
colorspace           NA                                                            
commonmark           NA                                                            
compiler             NA                                                            
compositions         NA                                                            
contfrac             NA                                                            
correlation          NA                                                            
cpp11                NA                                                            
crayon               NA                                                            
credentials          NA                                                            
curl                 NA                                                            
dada2                "Rcpp, RcppParallel"                                          
data.table           NA                                                            
datasets             NA                                                            
datawizard           NA                                                            
DBI                  NA                                                            
dbplyr               NA                                                            
DECIPHER             "Biostrings, S4Vectors, IRanges, XVector"                     
DelayedArray         "S4Vectors"                                                   
deldir               NA                                                            
                     Suggests                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
ade4                 "ade4TkGUI, adegraphics, adephylo, ape, CircStats, deldir,\nlattice, spdep, splancs, waveslim, progress, foreach, parallel,\ndoParallel, iterators"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
ambient              "covr"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
AnnotationDbi        "hgu95av2.db, GO.db, org.Sc.sgd.db, org.At.tair.db, RUnit,\nTxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, reactome.db,\nAnnotationForge, graph, EnsDb.Hsapiens.v75, BiocStyle, knitr"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
ape                  "gee, expm, igraph, phangorn"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
aplot                "ggtree"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
askpass              "testthat"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
assertthat           "testthat, covr"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
backports            NA                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
base                 "methods"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
base64enc            NA                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
BayesFactor          "doMC, foreach, testthat, knitr, markdown, arm, lme4, xtable,\nlanguageR"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
bayesm               "knitr, rmarkdown"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
bayestestR           "BayesFactor, bayesQR, bayesplot, BH, blavaan, bridgesampling,\nbrms, effectsize, emmeans, gamm4, ggdist, ggplot2, glmmTMB,\nhttr, KernSmooth, knitr, lavaan, lme4, logspline, MASS, mclust,\nmediation, modelbased, parameters, patchwork, performance,\nquadprog, posterior, RcppEigen, rmarkdown, rstan, rstanarm,\nsee, testthat, tweedie"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
BH                   NA                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
Biobase              "tools, tkWidgets, ALL, RUnit, golubEsets"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
BiocFileCache        "testthat, knitr, BiocStyle, rmarkdown, rtracklayer"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
BiocGenerics         "Biobase, S4Vectors, IRanges, GenomicRanges, DelayedArray,\nBiostrings, Rsamtools, AnnotationDbi, affy, affyPLM, DESeq2,\nflowClust, MSnbase, annotate, RUnit"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
BiocIO               "testthat, knitr, rmarkdown, BiocStyle"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
BiocManager          "BiocVersion, remotes, rmarkdown, testthat, withr, curl, knitr"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
BiocParallel         "BiocGenerics, tools, foreach, BatchJobs, BBmisc, doParallel,\nRmpi, GenomicRanges, RNAseqData.HNRNPC.bam.chr14,\nTxDb.Hsapiens.UCSC.hg19.knownGene, VariantAnnotation,\nRsamtools, GenomicAlignments, ShortRead, RUnit, BiocStyle,\nknitr, batchtools, data.table"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
BiocVersion          NA                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
biomaRt              "BiocStyle, knitr, rmarkdown, testthat, mockery"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
biomformat           "testthat (>= 0.10), knitr (>= 1.10), BiocStyle (>= 1.6),\nrmarkdown (>= 0.7)"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
Biostrings           "BSgenome (>= 1.13.14), BSgenome.Celegans.UCSC.ce2 (>=\n1.3.11), BSgenome.Dmelanogaster.UCSC.dm3 (>= 1.3.11),\nBSgenome.Hsapiens.UCSC.hg18, drosophila2probe, hgu95av2probe,\nhgu133aprobe, GenomicFeatures (>= 1.3.14), hgu95av2cdf, affy\n(>= 1.41.3), affydata (>= 1.11.5), RUnit"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
bit                  "testthat (>= 0.11.0), roxygen2, knitr, rmarkdown,\nmicrobenchmark, bit64 (>= 4.0.0), ff (>= 4.0.0)"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
bit64                NA                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
bitops               NA                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
blob                 "covr, crayon, pillar (>= 1.2.1), testthat"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
boot                 "MASS, survival"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
brew                 "testthat (>= 3.0.0)"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
brio                 "covr, testthat (>= 2.1.0)"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
broom                "AER, AUC, bbmle, betareg, biglm, binGroup, boot, btergm (>=\n1.10.6), car, carData, caret, cluster, cmprsk, coda, covr, drc,\ne1071, emmeans, epiR, ergm (>= 3.10.4), fixest (>= 0.9.0), gam\n(>= 1.15), gee, geepack, glmnet, glmnetUtils, gmm, Hmisc,\nirlba, interp, joineRML, Kendall, knitr, ks, Lahman, lavaan,\nleaps, lfe, lm.beta, lme4, lmodel2, lmtest (>= 0.9.38),\nlsmeans, maps, maptools, margins, MASS, mclust, mediation,\nmetafor, mfx, mgcv, mlogit, modeldata, modeltests, muhaz,\nmultcomp, network, nnet, orcutt (>= 2.2), ordinal, plm, poLCA,\npsych, quantreg, rgeos, rmarkdown, robust, robustbase, rsample,\nsandwich, sp, spdep (>= 1.1), spatialreg, speedglm, spelling,\nsurvey, survival, systemfit, testthat (>= 2.1.0), tseries,\nvars, zoo"                                                                                                                                                                                                                         
bslib                "shiny (>= 1.6.0), rmarkdown (>= 2.7), thematic, knitr,\ntestthat, withr, rappdirs, curl, magrittr"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
cachem               "testthat"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
callr                "cli (>= 1.1.0), covr, mockery, ps, rprojroot, spelling,\ntestthat (>= 3.0.0), withr (>= 2.3.0)"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
cellranger           "covr, testthat (>= 1.0.0), knitr, rmarkdown"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
class                NA                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
classInt             "spData (>= 0.2.6.2), units, knitr, rmarkdown"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
cli                  "callr, covr, digest, glue (>= 1.6.0), grDevices, htmltools,\nhtmlwidgets, knitr, methods, mockery, processx, ps (>=\n1.3.4.9000), rlang (>= 1.0.2.9003), rmarkdown, rprojroot,\nrstudioapi, testthat, tibble, whoami, withr"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
clipr                "covr, knitr, rmarkdown, rstudioapi (>= 0.5), testthat (>=\n2.0.0)"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
cluster              "MASS, Matrix"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
coda                 NA                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
codetools            NA                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
colorspace           "datasets, utils, KernSmooth, MASS, kernlab, mvtnorm, vcd,\ntcltk, shiny, shinyjs, ggplot2, dplyr, scales, grid, png, jpeg,\nknitr, rmarkdown, RColorBrewer, rcartocolor, scico, viridis,\nwesanderson"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
commonmark           "curl, testthat, xml2"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
compiler             NA                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
compositions         "rgl, combinat, energy, knitr, rmarkdown"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
contfrac             NA                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
correlation          "BayesFactor, poorman, energy, ggplot2, ggraph, gt, Hmisc,\nknitr, lme4, mbend, polycor, ppcor, psych, rmarkdown, rmcorr,\nrstanarm, see, testthat (>= 3.1.0), tidygraph, wdm, WRS2"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
cpp11                "bench, brio, callr, cli, covr, decor, desc, ggplot2, glue,\nknitr, lobstr, mockery, progress, rmarkdown, scales, Rcpp,\ntestthat, tibble, utils, vctrs, withr"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
crayon               "mockery, rstudioapi, testthat, withr"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
credentials          "testthat, knitr, rmarkdown"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
curl                 "spelling, testthat (>= 1.0.0), knitr, jsonlite, rmarkdown,\nmagrittr, httpuv (>= 1.4.4), webutils"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
dada2                "BiocStyle, knitr, rmarkdown"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
data.table           "bit64 (>= 4.0.0), bit (>= 4.0.4), curl, R.utils, xts,\nnanotime, zoo (>= 1.8-1), yaml, knitr, rmarkdown"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
datasets             NA                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
datawizard           "bayestestR, boot, brms, data.table, dplyr (>= 1.0),\neffectsize, gamm4, ggplot2, haven, htmltools, httr, knitr,\nlme4, mediation, parameters, poorman (>= 0.2.6), psych, readxl,\nreadr, rio, rmarkdown, rstanarm, see, testthat (>= 3.1.0),\ntidyr, withr"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
DBI                  "blob, covr, DBItest, dbplyr, downlit, dplyr, glue, hms,\nknitr, magrittr, RMariaDB, rmarkdown, rprojroot, RSQLite (>=\n1.1-2), testthat, xml2"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
dbplyr               "bit64, covr, knitr, Lahman, nycflights13, odbc, RMariaDB (>=\n1.0.2), rmarkdown, RPostgres (>= 1.1.3), RPostgreSQL, RSQLite\n(>= 2.1.0), testthat (>= 3.0.2), tidyr (>= 1.2.0)"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
DECIPHER             NA                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
DelayedArray         "BiocParallel, HDF5Array (>= 1.17.12), genefilter,\nSummarizedExperiment, airway, lobstr, DelayedMatrixStats,\nknitr, rmarkdown, BiocStyle, RUnit"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
deldir               "polyclip"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
                     Enhances                                                              License                                 
ade4                 NA                                                                    "GPL (>= 2)"                            
ambient              NA                                                                    "MIT + file LICENSE"                    
AnnotationDbi        NA                                                                    "Artistic-2.0"                          
ape                  NA                                                                    "GPL-2 | GPL-3"                         
aplot                NA                                                                    "Artistic-2.0"                          
askpass              NA                                                                    "MIT + file LICENSE"                    
assertthat           NA                                                                    "GPL-3"                                 
backports            NA                                                                    "GPL-2 | GPL-3"                         
base                 NA                                                                    "Part of R 4.2.1"                       
base64enc            "png"                                                                 "GPL-2 | GPL-3"                         
BayesFactor          NA                                                                    "GPL-2"                                 
bayesm               NA                                                                    "GPL (>= 2)"                            
bayestestR           NA                                                                    "GPL-3"                                 
BH                   NA                                                                    "BSL-1.0"                               
Biobase              NA                                                                    "Artistic-2.0"                          
BiocFileCache        NA                                                                    "Artistic-2.0"                          
BiocGenerics         NA                                                                    "Artistic-2.0"                          
BiocIO               NA                                                                    "Artistic-2.0"                          
BiocManager          NA                                                                    "Artistic-2.0"                          
BiocParallel         NA                                                                    "GPL-2 | GPL-3"                         
BiocVersion          NA                                                                    "Artistic-2.0"                          
biomaRt              NA                                                                    "Artistic-2.0"                          
biomformat           NA                                                                    "GPL-2"                                 
Biostrings           "Rmpi"                                                                "Artistic-2.0"                          
bit                  NA                                                                    "GPL-2 | GPL-3"                         
bit64                NA                                                                    "GPL-2 | GPL-3"                         
bitops               NA                                                                    "GPL (>= 2)"                            
blob                 NA                                                                    "MIT + file LICENSE"                    
boot                 NA                                                                    "Unlimited"                             
brew                 NA                                                                    "GPL-2"                                 
brio                 NA                                                                    "MIT + file LICENSE"                    
broom                NA                                                                    "MIT + file LICENSE"                    
bslib                NA                                                                    "MIT + file LICENSE"                    
cachem               NA                                                                    "MIT + file LICENSE"                    
callr                NA                                                                    "MIT + file LICENSE"                    
cellranger           NA                                                                    "MIT + file LICENSE"                    
class                NA                                                                    "GPL-2 | GPL-3"                         
classInt             NA                                                                    "GPL (>= 2)"                            
cli                  NA                                                                    "MIT + file LICENSE"                    
clipr                NA                                                                    "GPL-3"                                 
cluster              NA                                                                    "GPL (>= 2)"                            
coda                 NA                                                                    "GPL (>= 2)"                            
codetools            NA                                                                    "GPL"                                   
colorspace           NA                                                                    "BSD_3_clause + file LICENSE"           
commonmark           NA                                                                    "BSD_2_clause + file LICENSE"           
compiler             NA                                                                    "Part of R 4.2.1"                       
compositions         NA                                                                    "GPL (>= 2)"                            
contfrac             NA                                                                    "GPL-2"                                 
correlation          NA                                                                    "GPL-3"                                 
cpp11                NA                                                                    "MIT + file LICENSE"                    
crayon               NA                                                                    "MIT + file LICENSE"                    
credentials          NA                                                                    "MIT + file LICENSE"                    
curl                 NA                                                                    "MIT + file LICENSE"                    
dada2                NA                                                                    "LGPL-2"                                
data.table           NA                                                                    "MPL-2.0 | file LICENSE"                
datasets             NA                                                                    "Part of R 4.2.1"                       
datawizard           NA                                                                    "GPL (>= 3)"                            
DBI                  NA                                                                    "LGPL (>= 2.1)"                         
dbplyr               NA                                                                    "MIT + file LICENSE"                    
DECIPHER             NA                                                                    "GPL-3"                                 
DelayedArray         NA                                                                    "Artistic-2.0"                          
deldir               NA                                                                    "GPL (>= 2)"                            
                     License_is_FOSS License_restricts_use OS_type MD5sum NeedsCompilation Built  
ade4                 NA              NA                    NA      NA     "yes"            "4.2.0"
ambient              NA              NA                    NA      NA     "yes"            "4.2.0"
AnnotationDbi        NA              NA                    NA      NA     "no"             "4.2.0"
ape                  NA              NA                    NA      NA     "yes"            "4.2.0"
aplot                NA              NA                    NA      NA     "no"             "4.2.0"
askpass              NA              NA                    NA      NA     "yes"            "4.2.0"
assertthat           NA              NA                    NA      NA     "no"             "4.2.0"
backports            NA              NA                    NA      NA     "yes"            "4.2.0"
base                 NA              NA                    NA      NA     NA               "4.2.1"
base64enc            NA              NA                    NA      NA     "yes"            "4.2.0"
BayesFactor          NA              NA                    NA      NA     "yes"            "4.2.0"
bayesm               NA              NA                    NA      NA     "yes"            "4.2.0"
bayestestR           NA              NA                    NA      NA     "no"             "4.2.0"
BH                   NA              NA                    NA      NA     "no"             "4.2.0"
Biobase              NA              NA                    NA      NA     "yes"            "4.2.0"
BiocFileCache        NA              NA                    NA      NA     "no"             "4.2.0"
BiocGenerics         NA              NA                    NA      NA     "no"             "4.2.0"
BiocIO               NA              NA                    NA      NA     "no"             "4.2.0"
BiocManager          NA              NA                    NA      NA     "no"             "4.2.0"
BiocParallel         NA              NA                    NA      NA     "yes"            "4.2.1"
BiocVersion          NA              NA                    NA      NA     "no"             "4.2.0"
biomaRt              NA              NA                    NA      NA     "no"             "4.2.0"
biomformat           NA              NA                    NA      NA     "no"             "4.2.0"
Biostrings           NA              NA                    NA      NA     "yes"            "4.2.1"
bit                  NA              NA                    NA      NA     "yes"            "4.2.0"
bit64                NA              NA                    NA      NA     "yes"            "4.2.0"
bitops               NA              NA                    NA      NA     "yes"            "4.2.0"
blob                 NA              NA                    NA      NA     "no"             "4.2.0"
boot                 NA              NA                    NA      NA     "no"             "4.2.1"
brew                 NA              NA                    NA      NA     "no"             "4.2.0"
brio                 NA              NA                    NA      NA     "yes"            "4.2.0"
broom                NA              NA                    NA      NA     "no"             "4.2.0"
bslib                NA              NA                    NA      NA     "no"             "4.2.0"
cachem               NA              NA                    NA      NA     "yes"            "4.2.0"
callr                NA              NA                    NA      NA     "no"             "4.2.0"
cellranger           NA              NA                    NA      NA     "no"             "4.2.0"
class                NA              NA                    NA      NA     "yes"            "4.2.1"
classInt             NA              NA                    NA      NA     "yes"            "4.2.0"
cli                  NA              NA                    NA      NA     "yes"            "4.2.0"
clipr                NA              NA                    NA      NA     "no"             "4.2.0"
cluster              NA              NA                    NA      NA     "yes"            "4.2.0"
coda                 NA              NA                    NA      NA     "no"             "4.2.0"
codetools            NA              NA                    NA      NA     "no"             "4.2.1"
colorspace           NA              NA                    NA      NA     "yes"            "4.2.0"
commonmark           NA              NA                    NA      NA     "yes"            "4.2.0"
compiler             NA              NA                    NA      NA     NA               "4.2.1"
compositions         NA              NA                    NA      NA     "yes"            "4.2.0"
contfrac             NA              NA                    NA      NA     "yes"            "4.2.0"
correlation          NA              NA                    NA      NA     "no"             "4.2.0"
cpp11                NA              NA                    NA      NA     "no"             "4.2.1"
crayon               NA              NA                    NA      NA     "no"             "4.2.0"
credentials          NA              NA                    NA      NA     "no"             "4.2.0"
curl                 NA              NA                    NA      NA     "yes"            "4.2.0"
dada2                NA              NA                    NA      NA     "yes"            "4.2.0"
data.table           NA              NA                    NA      NA     "yes"            "4.2.1"
datasets             NA              NA                    NA      NA     NA               "4.2.1"
datawizard           NA              NA                    NA      NA     "no"             "4.2.0"
DBI                  NA              NA                    NA      NA     "no"             "4.2.0"
dbplyr               NA              NA                    NA      NA     "no"             "4.2.0"
DECIPHER             NA              NA                    NA      NA     "yes"            "4.2.0"
DelayedArray         NA              NA                    NA      NA     "yes"            "4.2.0"
deldir               NA              NA                    NA      NA     "yes"            "4.2.0"
 [ reached getOption("max.print") -- omitted 257 rows ]
installed.packages("vegan", dependencies=TRUE)
     Package LibPath Version Priority Depends Imports LinkingTo Suggests Enhances License License_is_FOSS License_restricts_use
     OS_type Archs MD5sum NeedsCompilation Built

Project Management

  1. Set up management structure (i.e., “data”, “src [source]”, “results”, “doc”). Basic folders you should have when doing data analysis.
  2. Avoiding redundancy of files
  3. Make sure to use version control (i.e., Git)

Getting Help

If you don’t know what a command does, just place a question mark (?) infront of the command:

?plot

You can also use the help command:

help()

You can even use it with symbols:

#? <-
?"<-"

Can get vignette:

vignette("FAQ-vegan")

To get citations:

citation("vegan")

To cite package ‘vegan’ in publications use:

  Oksanen J, Simpson G, Blanchet F, Kindt R, Legendre P, Minchin P, O'Hara R, Solymos P, Stevens M, Szoecs E, Wagner H,
  Barbour M, Bedward M, Bolker B, Borcard D, Carvalho G, Chirico M, De Caceres M, Durand S, Evangelista H, FitzJohn R,
  Friendly M, Furneaux B, Hannigan G, Hill M, Lahti L, McGlinn D, Ouellette M, Ribeiro Cunha E, Smith T, Stier A, Ter Braak
  C, Weedon J (2022). _vegan: Community Ecology Package_. R package version 2.6-2,
  <https://CRAN.R-project.org/package=vegan>.

A BibTeX entry for LaTeX users is

  @Manual{,
    title = {vegan: Community Ecology Package},
    author = {Jari Oksanen and Gavin L. Simpson and F. Guillaume Blanchet and Roeland Kindt and Pierre Legendre and Peter R. Minchin and R.B. O'Hara and Peter Solymos and M. Henry H. Stevens and Eduard Szoecs and Helene Wagner and Matt Barbour and Michael Bedward and Ben Bolker and Daniel Borcard and Gustavo Carvalho and Michael Chirico and Miquel {De Caceres} and Sebastien Durand and Heloisa Beatriz Antoniazi Evangelista and Rich FitzJohn and Michael Friendly and Brendan Furneaux and Geoffrey Hannigan and Mark O. Hill and Leo Lahti and Dan McGlinn and Marie-Helene Ouellette and Eduardo {Ribeiro Cunha} and Tyler Smith and Adrian Stier and Cajo J.F. {Ter Braak} and James Weedon},
    year = {2022},
    note = {R package version 2.6-2},
    url = {https://CRAN.R-project.org/package=vegan},
  }

Data and Their Formats

data.frame makes a spreadsheet (like in python)

cats <- data.frame(coat = c("calico", "black", "tabby"), weight = c(2.1,5,3.2), likes_string = c(1,0,1))
cats
getwd()
[1] "/Users/maggieshostak/Desktop/Practical Computing/Notes"

To create a new column, use cbind:

logweight <- log(cats$weight)
cbind(cats,logweight)

To print a string of text, use “paste” commmand:

paste("My cat is ", cats$coat, ", and it weighs ", cats$weight, " kg.", sep = "")
[1] "My cat is calico, and it weighs 2.1 kg." "My cat is black, and it weighs 5 kg."    "My cat is tabby, and it weighs 3.2 kg." 

Data Types

typeof(cats$coat)
[1] "character"
typeof(cats$weight)
[1] "double"

A double represent a numver with decimal places

typeof(cats$likes_string)
[1] "double"
typeof(3.14159)
[1] "double"
typeof(1i)
[1] "complex"

You can use “TRUE” & “FALSE”

typeof(TRUE)
[1] "logical"
typeof(T)
[1] "logical"
typeof(FALSE)
[1] "logical"
typeof(F)
[1] "logical"
typeof(cats)
[1] "list"
class(cats)
[1] "data.frame"

To open a file use:

file.show()

To make 1=TRUE & 0=FALSE

cats$likes_string <- as.logical(cats$likes_string)
typeof(cats$likes_string)
[1] "logical"
cats$likes_string
[1]  TRUE FALSE  TRUE
c("a", "b")
[1] "a" "b"
ab <-c("a","b")
ab
[1] "a" "b"
c(ab, "c")
[1] "a" "b" "c"
c(ab, ab)
[1] "a" "b" "a" "b"

To get a range, just use a colon (:)

1:10
 [1]  1  2  3  4  5  6  7  8  9 10

You can also use seq(#):

seq(10)
 [1]  1  2  3  4  5  6  7  8  9 10
z <- seq(10)
head(z, n=3)
[1] 1 2 3
length(z)
[1] 10
class(z)
[1] "integer"
typeof(z)
[1] "integer"
seq(1,100, by=5)
 [1]  1  6 11 16 21 26 31 36 41 46 51 56 61 66 71 76 81 86 91 96

Gives you 1 to 100 in intervals of 5

seq(70,100, by=5)
[1]  70  75  80  85  90  95 100

Data Frames

cats <- cbind(cats,logweight)
cats
str(cats$coat)
 chr [1:3] "calico" "black" "tabby"
str(cats$coat)
 chr [1:3] "calico" "black" "tabby"
coats <- "tabby", "tortoiseshell" "tortoiseshell", "black", "tabby"
Error: unexpected ',' in "coats <- "tabby","
factor("coats")
[1] coats
Levels: coats
categories <- factor(coats)
Error in factor(coats) : object 'coats' not found

Lists

list_example <- list(title="Numbers", numbers=1:10, data=TRUE)
list_example
$title
[1] "Numbers"

$numbers
 [1]  1  2  3  4  5  6  7  8  9 10

$data
[1] TRUE
another_list <- list(1,"a", TRUE, 1+1i)
another_list
[[1]]
[1] 1

[[2]]
[1] "a"

[[3]]
[1] TRUE

[[4]]
[1] 1+1i
typeof(list_example)
[1] "list"
class(list_example)
[1] "list"
typeof(another_list)
[1] "list"
class(another_list)
[1] "list"
typeof(cats)
[1] "list"
class(cats)
[1] "data.frame"

To turrn lists -> data.frame

data.frame(list_example)
data.frame(another_list)

To subset lists, # after comma means look at colomuns, # before means look at row:

cats
cats[,3]
[1]  TRUE FALSE  TRUE
cats[3,]
cats[2:3,c(1,3)]

Matrices

Matrix: made for math, all numbers

Data.frame/spreadsheet: can be quantitative or qualitative

matrix_example <- matrix(0,ncol=5, nrow=3)
matrix_example
     [,1] [,2] [,3] [,4] [,5]
[1,]    0    0    0    0    0
[2,]    0    0    0    0    0
[3,]    0    0    0    0    0
class(matrix_example)
[1] "matrix" "array" 
typeof(matrix_example)
[1] "double"
str(matrix_example)
 num [1:3, 1:5] 0 0 0 0 0 0 0 0 0 0 ...
dim(matrix_example)
[1] 3 5
ncol(matrix_example)
[1] 5
nrow(matrix_example)
[1] 3

To turn a matrix into a spreadsheet

class(data.frame(matrix_example))
[1] "data.frame"

To save as a data.frame

df_example <- data.frame(matrix_example)
df_example

Subsetting

Works with dataframes & matrices

p
[1]  2.3  6.9  4.0 23.0  1.0

TO apply names to vector use:

names(p) <- c('a', 'b', 'c', 'd', 'e')
p
   a    b    c    d    e 
 2.3  6.9  4.0 23.0  1.0 
p[1]
  a 
2.3 
p[2:4]
   b    c    d 
 6.9  4.0 23.0 
p[c(1,5)]
  a   e 
2.3 1.0 
p[c(1,1,1,3,4,5)]
   a    a    a    c    d    e 
 2.3  2.3  2.3  4.0 23.0  1.0 

To remove columns, use a (-)

p[-3]
   a    b    d    e 
 2.3  6.9 23.0  1.0 
p[c(-1,-5)]
   b    c    d 
 6.9  4.0 23.0 
p[-(2:4)]
  a   e 
2.3 1.0 
p[c('a','c')]
  a   c 
2.3 4.0 

To say not equal to, use !=

p[names(p) !='c']
   a    b    d    e 
 2.3  6.9 23.0  1.0 

Factors

f <- factor(c('a', 'b', 'c','d', 'e'))
f
[1] a b c d e
Levels: a b c d e

To do absolutely is equal to, use double =’s

f[f == 'a']
[1] a
Levels: a b c d e
f[1:3]
[1] a b c
Levels: a b c d e

To see if the factor contains some option, use %in%

f[f %in% c('b','c')]
[1] b c
Levels: a b c d e
f[-3]
[1] a b d e
Levels: a b c d e
f2
[1] a a b c c
Levels: a b c
f2[f2 == 'a']
[1] a a
Levels: a b c
f2 [f2 %in% c('a','c')]
[1] a a c c
Levels: a b c

Matrices Resumed

Setting the seed will make sure you get the same result everytime.

set.seed(65)
m <- matrix(rnorm(6*4), ncol=4, nrow=6)
m
           [,1]       [,2]       [,3]
[1,] -1.1968205 -0.3943568  0.4232027
[2,] -0.9516674 -1.2484030 -1.8461725
[3,]  0.2786364 -0.6521289 -0.2456747
[4,] -1.4449411 -1.1707346  1.2538299
[5,]  0.8216518  0.3604497  1.5633419
[6,]  1.2470188  1.2302708 -1.2644661
            [,4]
[1,] -2.34367583
[2,] -0.77605977
[3,] -2.16173144
[4,]  0.05701057
[5,] -0.24867199
[6,] -0.07830796

Slicing Matrices

For specific rows

m[3:4, c(3,1)]
           [,1]       [,2]
[1,] -0.2456747  0.2786364
[2,]  1.2538299 -1.4449411

For specific columns

m[,c(3,4)]
           [,1]        [,2]
[1,]  0.4232027 -2.34367583
[2,] -1.8461725 -0.77605977
[3,] -0.2456747 -2.16173144
[4,]  1.2538299  0.05701057
[5,]  1.5633419 -0.24867199
[6,] -1.2644661 -0.07830796

Lists

xlist <- list(a="BIOL48006220", b=seq(1,10, by = 0.5), data="Grades")
xlist
$a
[1] "BIOL48006220"

$b
 [1]  1.0  1.5  2.0  2.5  3.0  3.5  4.0  4.5
 [9]  5.0  5.5  6.0  6.5  7.0  7.5  8.0  8.5
[17]  9.0  9.5 10.0

$data
[1] "Grades"

by = 0.5 is step size/increment

xlist[1:2]
$a
[1] "BIOL48006220"

$b
 [1]  1.0  1.5  2.0  2.5  3.0  3.5  4.0  4.5
 [9]  5.0  5.5  6.0  6.5  7.0  7.5  8.0  8.5
[17]  9.0  9.5 10.0
xlist['a']
$a
[1] "BIOL48006220"

You can also subslice by using [[]] to represent just the value not the object

xlist[['a']]
[1] "BIOL48006220"
xlist['b']
$b
 [1]  1.0  1.5  2.0  2.5  3.0  3.5  4.0  4.5
 [9]  5.0  5.5  6.0  6.5  7.0  7.5  8.0  8.5
[17]  9.0  9.5 10.0
xlist[['b']]
 [1]  1.0  1.5  2.0  2.5  3.0  3.5  4.0  4.5
 [9]  5.0  5.5  6.0  6.5  7.0  7.5  8.0  8.5
[17]  9.0  9.5 10.0

You can use a $ to represent what ever the values are:

xlist$b
 [1]  1.0  1.5  2.0  2.5  3.0  3.5  4.0  4.5
 [9]  5.0  5.5  6.0  6.5  7.0  7.5  8.0  8.5
[17]  9.0  9.5 10.0

Date Frames

gp <- read.csv('/Users/maggieshostak/Desktop/Practical\ Computing/Class\ Examples/PracticalComputing_2022/data/forest_area_sq_km.csv')
head(gp, n=10L)

To determine how many rows

nrow(gp)
[1] 214
head(gp[["country"]], 10L)
 [1] "Aruba"               
 [2] "Afghanistan"         
 [3] "Angola"              
 [4] "Albania"             
 [5] "Andorra"             
 [6] "United Arab Emirates"
 [7] "Argentina"           
 [8] "Armenia"             
 [9] "American Samoa"      
[10] "Antigua and Barbuda" 
gp$X1997
  [1] "4.2"   "12.1k" "780k"  "7730" 
  [5] "160"   "2970"  "337k"  "3330" 
  [9] "178"   "95.8"  "1.32M" "38.3k"
 [13] "9790"  "2100"  "7560"  "42.8k"
 [17] "73.2k" "19.2k" "33.7k" "3.4"  
 [21] "5100"  "21.3k" "81.7k" "14.9k"
 [25] "10"    "556k"  "5.59M" "63"   
 [29] "4000"  "25.9k" "179k"  "230k" 
 [33] "3.48M" "8.3"   "11.9k" "157k" 
 [37] "1.73M" "56.5k" "218k"  "1.45M"
 [41] "222k"  "632k"  "426"   "349"  
 [45] "28.7k" "23.6k" "130"   "1700" 
 [49] "26.4k" "113k"  "56"    "484"  
 [53] "5640"  "19k"   "16k"   "139k" 
 [57] "561"   "11.2k" "165k"  "22.3k"
 [61] "187k"  "223k"  "9930"  "151k" 
 [65] "0.8"   "638"   "237k"  "34.6" 
 [69] "29.2k" "27.6k" "90.6k" "0"    
 [73] "70k"   "3690"  "21.7k" "26.3k"
 [77] "35.4k" "177"   "2.2"   "43.2k"
 [81] "240"   "186k"  "68.2k" "18.8k"
 [85] "3810"  "19k"   "1.05M" "669k" 
 [89] "5970"  "92.8k" "8150"  "273"  
 [93] "1490"  "82.1k" "5210"  "975"  
 [97] "249k"  "31.6k" "39.4k" "11.7k"
[101] "108k"  "11.8"  "110"   "64.9k"
[105] "45.7"  "175k"  "1380"  "82.8k"
[109] "2170"  "211"   "66.6"  "22k"  
[113] "345"   "20.1k" "870"   "32.3k"
[117] "10"    "55k"   "0"     "3410" 
[121] "132k"  "8.2"   "688k"  "94"   
[125] "9480"  "133k"  "3.5"   "357k" 
[129] "6260"  "143k"  "323"   "416k" 
[133] "4330"  "418"   "31.7k" "199k" 
[137] "82k"   "8370"  "14.5k" "252k" 
[141] "56k"   "3570"  ""      "121k" 
[145] "57.6k" "0"     "97.5k" "30"   
[149] "46.1k" "44.8k" "755k"  "74k"  
[153] "393"   "363k"  "90.2k" "4070" 
[157] "65.5k" "33k"   "235k"  "90.8" 
[161] "1480"  "0"     "63.7k" "8.09M"
[165] "2930"  "9770"  ""      "89.4k"
[169] "166"   "25.4k" "29.7k" "6830" 
[173] "10"    "76.7k" "24.8k" ""     
[177] "584"   "153k"  "19k"   "12.2k"
[181] "281k"  "4710"  ""      "337"  
[185] "4200"  "105"   "64.3k" "12.9k"
[189] "191k"  "4100"  "41.3k" "9520" 
[193] "89.5"  "2380"  "6630"  "201k" 
[197] "10"    "544k"  "32.5k" "94.6k"
[201] "12.5k" "3.03M" "28.8k" "283"  
[205] "497k"  "36.8"  "213"   "113k" 
[209] "4420"  "1720"  "5490"  "179k" 
[213] "471k"  "185k" 

To just look at rows 1-3 & columns 2-5

To just look at columns 1 & 3 & 4 & 5

Conditionals & Flow

To indent we use { then press enter to make conditional statement:

  print("n is equal to 10")
[1] "n is equal to 10"
for (n in seq(1,20)) {
  if (n<10) {
    print("n is less than 10")
  } else if (n>10) {
    print("n is more than 10")
  } else {
    print("n is equal to 10")
  }
}
[1] "n is less than 10"
[1] "n is less than 10"
[1] "n is less than 10"
[1] "n is less than 10"
[1] "n is less than 10"
[1] "n is less than 10"
[1] "n is less than 10"
[1] "n is less than 10"
[1] "n is less than 10"
[1] "n is equal to 10"
[1] "n is more than 10"
[1] "n is more than 10"
[1] "n is more than 10"
[1] "n is more than 10"
[1] "n is more than 10"
[1] "n is more than 10"
[1] "n is more than 10"
[1] "n is more than 10"
[1] "n is more than 10"
[1] "n is more than 10"

Paste is like the cat command:

g <- 0

while (g <=10) {
  print(paste(g, "is less than or equal to 10"))
  g <- g+1
}
[1] "0 is less than or equal to 10"
[1] "1 is less than or equal to 10"
[1] "2 is less than or equal to 10"
[1] "3 is less than or equal to 10"
[1] "4 is less than or equal to 10"
[1] "5 is less than or equal to 10"
[1] "6 is less than or equal to 10"
[1] "7 is less than or equal to 10"
[1] "8 is less than or equal to 10"
[1] "9 is less than or equal to 10"
[1] "10 is less than or equal to 10"

Plotting & Figures

installed.packages('ggplot2')
     Package LibPath Version Priority
     Depends Imports LinkingTo Suggests
     Enhances License License_is_FOSS
     License_restricts_use OS_type Archs
     MD5sum NeedsCompilation Built
library(ggplot2)
gp <- read.csv('/Users/maggieshostak/Desktop/Practical\ Computing/Class\ Examples/PracticalComputing_2022/data/gapminder_all.csv')

head(gp)
ggplot(data=gp, mapping=aes(x=gdpPercap_1952, y=pop_1952)) + geom_point()

gapminder <- read.csv("https://raw.githubusercontent.com/swcarpentry/r-novice-gapminder/gh-pages/_episodes_rmd/data/gapminder_data.csv")
head(gapminder)
ggplot(data=gapminder, mapping=aes(x=gdpPercap, y=lifeExp)) + geom_point()

ggplot(data=gapminder, mapping=aes(x=year, y=lifeExp, by=country, color=continent)) + geom_line()

To transfer an exponential model, use the log10:

Africas <- gapminder[gapminder$continent == "Africa", ]
head(Africas)
NA

Facet_wrap: tells you how you want to plot them independetly

ggplot(data=Africas, mapping=aes(x=year, y=lifeExp)) +
  geom_line() +
  facet_wrap(~ country)

How to save a graph to make an output file:

AfricanLifeExpectancy <- ggplot(data=Africas, mapping=aes(x=year, y=lifeExp)) +
  geom_line(color="red") +
  facet_wrap(~ country) +
  theme(axis.text.x = element_text(angle=90)) +
  labs(
    x="Year",
    Y="lifeExp",
    Title="Life Expectency Over Time in African Countries",
  )
ggsave(filename="data/AfricanLifeExpectancy.png", plot=AfricanLifeExpectancy, width=24, height=40, dpi=300, units="cm")
pdf(file="results/AfricanLifeExp.pdf", width=24, height=40)
Error in pdf(file = "results/AfricanLifeExp.pdf", width = 24, height = 40) : 
  cannot open file 'results/AfricanLifeExp.pdf'
write.table(gapminder, file="data/gapminder_web.csv", sep=",")
write.csv(Africas, file="data/gapmminder_web_africas.csv")

Fancy Plots

install.packages(c("ggridges", "viridis", "hrbrthemes", dependencies=T))
Warning in install.packages :
  package ‘TRUE’ is not available for this version of R

A version of this package for your version of R might be available elsewhere,
see the ideas at
https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages
also installing the dependencies ‘gridExtra’, ‘gdtools’

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/gridExtra_2.3.tgz'
Content type 'application/x-gzip' length 1103175 bytes (1.1 MB)
==================================================
downloaded 1.1 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/gdtools_0.2.4.tgz'
Content type 'application/x-gzip' length 1921424 bytes (1.8 MB)
==================================================
downloaded 1.8 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/ggridges_0.5.4.tgz'
Content type 'application/x-gzip' length 2254162 bytes (2.1 MB)
==================================================
downloaded 2.1 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/viridis_0.6.2.tgz'
Content type 'application/x-gzip' length 2998780 bytes (2.9 MB)
==================================================
downloaded 2.9 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/hrbrthemes_0.8.0.tgz'
Content type 'application/x-gzip' length 2291025 bytes (2.2 MB)
==================================================
downloaded 2.2 MB

The downloaded binary packages are in
    /var/folders/jq/7jw4lmyx39n4m1jf7hb6v0t80000gn/T//RtmprpsOn3/downloaded_packages
library(hrbrthemes)
Registered S3 methods overwritten by 'htmltools':
  method               from         
  print.html           tools:rstudio
  print.shiny.tag      tools:rstudio
  print.shiny.tag.list tools:rstudio
NOTE: Either Arial Narrow or Roboto Condensed fonts are required to use these themes.
      Please use hrbrthemes::import_roboto_condensed() to install Roboto Condensed and
      if Arial Narrow is not on your system, please see https://bit.ly/arialnarrow
hrbrthemes::import_roboto_condensed()
sh: line 1:  2974 Segmentation fault: 11  '/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rttf2pt1/exec//ttf2pt1' -a -GfAe '/Library/Frameworks/R.framework/Versions/4.2/Resources/library/hrbrthemes/fonts/roboto-condensed/RobotoCondensed-Bold.ttf' '/var/folders/jq/7jw4lmyx39n4m1jf7hb6v0t80000gn/T//RtmprpsOn3/fonts/RobotoCondensed-Bold' 2>&1
sh: line 1:  2977 Segmentation fault: 11  '/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rttf2pt1/exec//ttf2pt1' -a -GfAe '/Library/Frameworks/R.framework/Versions/4.2/Resources/library/hrbrthemes/fonts/roboto-condensed/RobotoCondensed-Light.ttf' '/var/folders/jq/7jw4lmyx39n4m1jf7hb6v0t80000gn/T//RtmprpsOn3/fonts/RobotoCondensed-Light' 2>&1
sh: line 1:  2979 Segmentation fault: 11  '/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rttf2pt1/exec//ttf2pt1' -a -GfAe '/Library/Frameworks/R.framework/Versions/4.2/Resources/library/hrbrthemes/fonts/roboto-condensed/RobotoCondensed-Regular.ttf' '/var/folders/jq/7jw4lmyx39n4m1jf7hb6v0t80000gn/T//RtmprpsOn3/fonts/RobotoCondensed-Regular' 2>&1
You will likely need to install these fonts on your system as well.

You can find them in [/Library/Frameworks/R.framework/Versions/4.2/Resources/library/hrbrthemes/fonts/roboto-condensed]

..x.. makes it a gradient fill & smooth

ggplot(lincoln_weather, aes(x=`Mean Temperature[F]`, y= `Month`, fill=..x..)) + geom_density_ridges_gradient(scale = 3, rel_min_height = 0.01) + scale_fill_viridis(name="temp. [F]", option = "A") + theme_ipsum() +
  theme(
    legend.position="none",
    panel.spacing = unit(0.1, "lines"),
    strip.text.x = element_text(size=8))
Error in ggplot(lincoln_weather, aes(x = `Mean Temperature[F]`, y = Month,  : 
  could not find function "ggplot"

Themes dictate fonts

Taking family and year described, use bin to make a hard/bar plot

install.packages(c("ggstatsplot", "palmerpenguins", dependencies=T))
Warning in install.packages :
  package ‘TRUE’ is not available for this version of R

A version of this package for your version of R might be available elsewhere,
see the ideas at
https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages
also installing the dependencies ‘elliptic’, ‘contfrac’, ‘deSolve’, ‘coda’, ‘pbapply’, ‘mvtnorm’, ‘MatrixModels’, ‘hypergeo’, ‘reshape’, ‘mc2d’, ‘bayestestR’, ‘prismatic’, ‘BayesFactor’, ‘effectsize’, ‘WRS2’, ‘zeallot’, ‘correlation’, ‘datawizard’, ‘ggrepel’, ‘ggsignif’, ‘insight’, ‘paletteer’, ‘parameters’, ‘performance’, ‘statsExpressions’

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/elliptic_1.4-0.tgz'
Content type 'application/x-gzip' length 1257923 bytes (1.2 MB)
==================================================
downloaded 1.2 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/contfrac_1.1-12.tgz'
Content type 'application/x-gzip' length 27492 bytes (26 KB)
==================================================
downloaded 26 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/deSolve_1.34.tgz'
Content type 'application/x-gzip' length 2619125 bytes (2.5 MB)
==================================================
downloaded 2.5 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/coda_0.19-4.tgz'
Content type 'application/x-gzip' length 321854 bytes (314 KB)
==================================================
downloaded 314 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/pbapply_1.5-0.tgz'
Content type 'application/x-gzip' length 76335 bytes (74 KB)
==================================================
downloaded 74 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/mvtnorm_1.1-3.tgz'
Content type 'application/x-gzip' length 260575 bytes (254 KB)
==================================================
downloaded 254 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/MatrixModels_0.5-1.tgz'
Content type 'application/x-gzip' length 435122 bytes (424 KB)
==================================================
downloaded 424 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/hypergeo_1.2-13.tgz'
Content type 'application/x-gzip' length 352373 bytes (344 KB)
==================================================
downloaded 344 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/reshape_0.8.9.tgz'
Content type 'application/x-gzip' length 168752 bytes (164 KB)
==================================================
downloaded 164 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/mc2d_0.1-21.tgz'
Content type 'application/x-gzip' length 1378438 bytes (1.3 MB)
==================================================
downloaded 1.3 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/bayestestR_0.13.0.tgz'
Content type 'application/x-gzip' length 1477700 bytes (1.4 MB)
==================================================
downloaded 1.4 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/prismatic_1.1.1.tgz'
Content type 'application/x-gzip' length 786489 bytes (768 KB)
==================================================
downloaded 768 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/BayesFactor_0.9.12-4.4.tgz'
Content type 'application/x-gzip' length 4278037 bytes (4.1 MB)
==================================================
downloaded 4.1 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/effectsize_0.8.1.tgz'
Content type 'application/x-gzip' length 680142 bytes (664 KB)
==================================================
downloaded 664 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/WRS2_1.1-4.tgz'
Content type 'application/x-gzip' length 965147 bytes (942 KB)
==================================================
downloaded 942 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/zeallot_0.1.0.tgz'
Content type 'application/x-gzip' length 57961 bytes (56 KB)
==================================================
downloaded 56 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/correlation_0.8.3.tgz'
Content type 'application/x-gzip' length 2528105 bytes (2.4 MB)
==================================================
downloaded 2.4 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/datawizard_0.6.3.tgz'
Content type 'application/x-gzip' length 1142513 bytes (1.1 MB)
==================================================
downloaded 1.1 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/ggrepel_0.9.1.tgz'
Content type 'application/x-gzip' length 710937 bytes (694 KB)
==================================================
downloaded 694 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/ggsignif_0.6.4.tgz'
Content type 'application/x-gzip' length 608262 bytes (594 KB)
==================================================
downloaded 594 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/insight_0.18.6.tgz'
Content type 'application/x-gzip' length 2004384 bytes (1.9 MB)
==================================================
downloaded 1.9 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/paletteer_1.5.0.tgz'
Content type 'application/x-gzip' length 432181 bytes (422 KB)
==================================================
downloaded 422 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/parameters_0.19.0.tgz'
Content type 'application/x-gzip' length 1861775 bytes (1.8 MB)
==================================================
downloaded 1.8 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/performance_0.10.0.tgz'
Content type 'application/x-gzip' length 3061327 bytes (2.9 MB)
==================================================
downloaded 2.9 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/statsExpressions_1.3.4.tgz'
Content type 'application/x-gzip' length 3392521 bytes (3.2 MB)
==================================================
downloaded 3.2 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/ggstatsplot_0.9.5.tgz'
Content type 'application/x-gzip' length 3422071 bytes (3.3 MB)
==================================================
downloaded 3.3 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/palmerpenguins_0.1.1.tgz'
Content type 'application/x-gzip' length 3003192 bytes (2.9 MB)
==================================================
downloaded 2.9 MB

The downloaded binary packages are in
    /var/folders/jq/7jw4lmyx39n4m1jf7hb6v0t80000gn/T//RtmprpsOn3/downloaded_packages
library(ggstatsplot)
You can cite this package as:
     Patil, I. (2021). Visualizations with statistical details: The 'ggstatsplot' approach.
     Journal of Open Source Software, 6(61), 3167, doi:10.21105/joss.03167
data("penguins", package = "palmerpenguins")
penguins
penguins2 <-  drop_na(penguins)
penguins2
plt <- ggbetweenstats(
  data = penguins,
  x=species,
  y=bill length)
Error: unexpected symbol in:
"  x=species,
  y=bill length"
gapminder2 <- drop_na(gapminder)
boxplot(gapminder2$lifeExp ~ gapminder2$continent)

Box plots don’t show distribution, instead use a violin plot

install.packages("vioplot", dependencies = T)
also installing the dependencies ‘sm’, ‘zoo’

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/sm_2.2-5.7.1.tgz'
Content type 'application/x-gzip' length 814173 bytes (795 KB)
==================================================
downloaded 795 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/zoo_1.8-11.tgz'
Content type 'application/x-gzip' length 1017258 bytes (993 KB)
==================================================
downloaded 993 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/vioplot_0.3.7.tgz'
Content type 'application/x-gzip' length 822536 bytes (803 KB)
==================================================
downloaded 803 KB

The downloaded binary packages are in
    /var/folders/jq/7jw4lmyx39n4m1jf7hb6v0t80000gn/T//RtmprpsOn3/downloaded_packages
library(vioplot)
Loading required package: sm
Package 'sm', version 2.2-5.7: type help(sm) for summary information
Loading required package: zoo

Attaching package: ‘zoo’

The following objects are masked from ‘package:base’:

    as.Date, as.Date.numeric

plt <- ggbetweenstats()
Error in assign(name, val, envir = env) : 
  argument "val" is missing, with no default

To save/export graph

ggsave(
  flename = "insert name",
  plot = plt
  width  = 8
Error: unexpected symbol in:
"  plot = plt
  width"

You can then load the stuff in InkScape to adjust the visual aesthetics

PCA Plots

For principle components, you need a matrix

penguins_matrix
       bill_length_mm bill_depth_mm flipper_length_mm body_mass_g
  [1,]           39.1          18.7               181        3750
  [2,]           39.5          17.4               186        3800
  [3,]           40.3          18.0               195        3250
  [4,]           36.7          19.3               193        3450
  [5,]           39.3          20.6               190        3650
  [6,]           38.9          17.8               181        3625
  [7,]           39.2          19.6               195        4675
  [8,]           41.1          17.6               182        3200
  [9,]           38.6          21.2               191        3800
 [10,]           34.6          21.1               198        4400
 [11,]           36.6          17.8               185        3700
 [12,]           38.7          19.0               195        3450
 [13,]           42.5          20.7               197        4500
 [14,]           34.4          18.4               184        3325
 [15,]           46.0          21.5               194        4200
 [16,]           37.8          18.3               174        3400
 [17,]           37.7          18.7               180        3600
 [18,]           35.9          19.2               189        3800
 [19,]           38.2          18.1               185        3950
 [20,]           38.8          17.2               180        3800
 [21,]           35.3          18.9               187        3800
 [22,]           40.6          18.6               183        3550
 [23,]           40.5          17.9               187        3200
 [24,]           37.9          18.6               172        3150
 [25,]           40.5          18.9               180        3950
 [26,]           39.5          16.7               178        3250
 [27,]           37.2          18.1               178        3900
 [28,]           39.5          17.8               188        3300
 [29,]           40.9          18.9               184        3900
 [30,]           36.4          17.0               195        3325
 [31,]           39.2          21.1               196        4150
 [32,]           38.8          20.0               190        3950
 [33,]           42.2          18.5               180        3550
 [34,]           37.6          19.3               181        3300
 [35,]           39.8          19.1               184        4650
 [36,]           36.5          18.0               182        3150
 [37,]           40.8          18.4               195        3900
 [38,]           36.0          18.5               186        3100
 [39,]           44.1          19.7               196        4400
 [40,]           37.0          16.9               185        3000
 [41,]           39.6          18.8               190        4600
 [42,]           41.1          19.0               182        3425
 [43,]           36.0          17.9               190        3450
 [44,]           42.3          21.2               191        4150
 [45,]           39.6          17.7               186        3500
 [46,]           40.1          18.9               188        4300
 [47,]           35.0          17.9               190        3450
 [48,]           42.0          19.5               200        4050
 [49,]           34.5          18.1               187        2900
 [50,]           41.4          18.6               191        3700
 [51,]           39.0          17.5               186        3550
 [52,]           40.6          18.8               193        3800
 [53,]           36.5          16.6               181        2850
 [54,]           37.6          19.1               194        3750
 [55,]           35.7          16.9               185        3150
 [56,]           41.3          21.1               195        4400
 [57,]           37.6          17.0               185        3600
 [58,]           41.1          18.2               192        4050
 [59,]           36.4          17.1               184        2850
 [60,]           41.6          18.0               192        3950
 [61,]           35.5          16.2               195        3350
 [62,]           41.1          19.1               188        4100
 [63,]           35.9          16.6               190        3050
 [64,]           41.8          19.4               198        4450
 [65,]           33.5          19.0               190        3600
 [66,]           39.7          18.4               190        3900
 [67,]           39.6          17.2               196        3550
 [68,]           45.8          18.9               197        4150
 [69,]           35.5          17.5               190        3700
 [70,]           42.8          18.5               195        4250
 [71,]           40.9          16.8               191        3700
 [72,]           37.2          19.4               184        3900
 [73,]           36.2          16.1               187        3550
 [74,]           42.1          19.1               195        4000
 [75,]           34.6          17.2               189        3200
 [76,]           42.9          17.6               196        4700
 [77,]           36.7          18.8               187        3800
 [78,]           35.1          19.4               193        4200
 [79,]           37.3          17.8               191        3350
 [80,]           41.3          20.3               194        3550
 [81,]           36.3          19.5               190        3800
 [82,]           36.9          18.6               189        3500
 [83,]           38.3          19.2               189        3950
 [84,]           38.9          18.8               190        3600
 [85,]           35.7          18.0               202        3550
 [86,]           41.1          18.1               205        4300
 [87,]           34.0          17.1               185        3400
 [88,]           39.6          18.1               186        4450
 [89,]           36.2          17.3               187        3300
 [90,]           40.8          18.9               208        4300
 [91,]           38.1          18.6               190        3700
 [92,]           40.3          18.5               196        4350
 [93,]           33.1          16.1               178        2900
 [94,]           43.2          18.5               192        4100
 [95,]           35.0          17.9               192        3725
 [96,]           41.0          20.0               203        4725
 [97,]           37.7          16.0               183        3075
 [98,]           37.8          20.0               190        4250
 [99,]           37.9          18.6               193        2925
[100,]           39.7          18.9               184        3550
[101,]           38.6          17.2               199        3750
[102,]           38.2          20.0               190        3900
[103,]           38.1          17.0               181        3175
[104,]           43.2          19.0               197        4775
[105,]           38.1          16.5               198        3825
[106,]           45.6          20.3               191        4600
[107,]           39.7          17.7               193        3200
[108,]           42.2          19.5               197        4275
[109,]           39.6          20.7               191        3900
[110,]           42.7          18.3               196        4075
[111,]           38.6          17.0               188        2900
[112,]           37.3          20.5               199        3775
[113,]           35.7          17.0               189        3350
[114,]           41.1          18.6               189        3325
[115,]           36.2          17.2               187        3150
[116,]           37.7          19.8               198        3500
[117,]           40.2          17.0               176        3450
[118,]           41.4          18.5               202        3875
[119,]           35.2          15.9               186        3050
[120,]           40.6          19.0               199        4000
[121,]           38.8          17.6               191        3275
[122,]           41.5          18.3               195        4300
[123,]           39.0          17.1               191        3050
[124,]           44.1          18.0               210        4000
[125,]           38.5          17.9               190        3325
[126,]           43.1          19.2               197        3500
[127,]           36.8          18.5               193        3500
[128,]           37.5          18.5               199        4475
[129,]           38.1          17.6               187        3425
[130,]           41.1          17.5               190        3900
[131,]           35.6          17.5               191        3175
[132,]           40.2          20.1               200        3975
[133,]           37.0          16.5               185        3400
[134,]           39.7          17.9               193        4250
[135,]           40.2          17.1               193        3400
[136,]           40.6          17.2               187        3475
[137,]           32.1          15.5               188        3050
[138,]           40.7          17.0               190        3725
[139,]           37.3          16.8               192        3000
[140,]           39.0          18.7               185        3650
[141,]           39.2          18.6               190        4250
[142,]           36.6          18.4               184        3475
[143,]           36.0          17.8               195        3450
[144,]           37.8          18.1               193        3750
[145,]           36.0          17.1               187        3700
[146,]           41.5          18.5               201        4000
[147,]           46.1          13.2               211        4500
[148,]           50.0          16.3               230        5700
[149,]           48.7          14.1               210        4450
[150,]           50.0          15.2               218        5700
[151,]           47.6          14.5               215        5400
[152,]           46.5          13.5               210        4550
[153,]           45.4          14.6               211        4800
[154,]           46.7          15.3               219        5200
[155,]           43.3          13.4               209        4400
[156,]           46.8          15.4               215        5150
[157,]           40.9          13.7               214        4650
[158,]           49.0          16.1               216        5550
[159,]           45.5          13.7               214        4650
[160,]           48.4          14.6               213        5850
[161,]           45.8          14.6               210        4200
[162,]           49.3          15.7               217        5850
[163,]           42.0          13.5               210        4150
[164,]           49.2          15.2               221        6300
[165,]           46.2          14.5               209        4800
[166,]           48.7          15.1               222        5350
[167,]           50.2          14.3               218        5700
[168,]           45.1          14.5               215        5000
[169,]           46.5          14.5               213        4400
[170,]           46.3          15.8               215        5050
[171,]           42.9          13.1               215        5000
[172,]           46.1          15.1               215        5100
[173,]           47.8          15.0               215        5650
[174,]           48.2          14.3               210        4600
[175,]           50.0          15.3               220        5550
[176,]           47.3          15.3               222        5250
[177,]           42.8          14.2               209        4700
[178,]           45.1          14.5               207        5050
[179,]           59.6          17.0               230        6050
[180,]           49.1          14.8               220        5150
[181,]           48.4          16.3               220        5400
[182,]           42.6          13.7               213        4950
[183,]           44.4          17.3               219        5250
[184,]           44.0          13.6               208        4350
[185,]           48.7          15.7               208        5350
[186,]           42.7          13.7               208        3950
[187,]           49.6          16.0               225        5700
[188,]           45.3          13.7               210        4300
[189,]           49.6          15.0               216        4750
[190,]           50.5          15.9               222        5550
[191,]           43.6          13.9               217        4900
[192,]           45.5          13.9               210        4200
[193,]           50.5          15.9               225        5400
[194,]           44.9          13.3               213        5100
[195,]           45.2          15.8               215        5300
[196,]           46.6          14.2               210        4850
[197,]           48.5          14.1               220        5300
[198,]           45.1          14.4               210        4400
[199,]           50.1          15.0               225        5000
[200,]           46.5          14.4               217        4900
[201,]           45.0          15.4               220        5050
[202,]           43.8          13.9               208        4300
[203,]           45.5          15.0               220        5000
[204,]           43.2          14.5               208        4450
[205,]           50.4          15.3               224        5550
[206,]           45.3          13.8               208        4200
[207,]           46.2          14.9               221        5300
[208,]           45.7          13.9               214        4400
[209,]           54.3          15.7               231        5650
[210,]           45.8          14.2               219        4700
[211,]           49.8          16.8               230        5700
[212,]           49.5          16.2               229        5800
[213,]           43.5          14.2               220        4700
[214,]           50.7          15.0               223        5550
[215,]           47.7          15.0               216        4750
[216,]           46.4          15.6               221        5000
[217,]           48.2          15.6               221        5100
[218,]           46.5          14.8               217        5200
[219,]           46.4          15.0               216        4700
[220,]           48.6          16.0               230        5800
[221,]           47.5          14.2               209        4600
[222,]           51.1          16.3               220        6000
[223,]           45.2          13.8               215        4750
[224,]           45.2          16.4               223        5950
[225,]           49.1          14.5               212        4625
[226,]           52.5          15.6               221        5450
[227,]           47.4          14.6               212        4725
[228,]           50.0          15.9               224        5350
[229,]           44.9          13.8               212        4750
[230,]           50.8          17.3               228        5600
[231,]           43.4          14.4               218        4600
[232,]           51.3          14.2               218        5300
[233,]           47.5          14.0               212        4875
[234,]           52.1          17.0               230        5550
[235,]           47.5          15.0               218        4950
[236,]           52.2          17.1               228        5400
[237,]           45.5          14.5               212        4750
[238,]           49.5          16.1               224        5650
[239,]           44.5          14.7               214        4850
[240,]           50.8          15.7               226        5200
[241,]           49.4          15.8               216        4925
[242,]           46.9          14.6               222        4875
[243,]           48.4          14.4               203        4625
[244,]           51.1          16.5               225        5250
[245,]           48.5          15.0               219        4850
[246,]           55.9          17.0               228        5600
[247,]           47.2          15.5               215        4975
[248,]           49.1          15.0               228        5500
[249,]           46.8          16.1               215        5500
[250,]           41.7          14.7               210        4700
 [ reached getOption("max.print") -- omitted 83 rows ]
row.names(penguins2) <-penguins2[,1]
Warning: Setting row names on a tibble is deprecated.Error in `.rowNamesDF<-`(x, value = value) : invalid 'row.names' length

Component 1 represents # of dimensions you have (x-axis, y-axis, z-axis & 4th-axes) and it rotates/interactions it based on categories [this will change the axes]

Individual Loadings

loadings(penguin_pca)

Loadings:
                  Comp.1 Comp.2 Comp.3 Comp.4
bill_length_mm     0.454  0.600  0.642  0.145
bill_depth_mm     -0.399  0.796 -0.426 -0.160
flipper_length_mm  0.577        -0.236 -0.782
body_mass_g        0.550        -0.592  0.585

               Comp.1 Comp.2 Comp.3 Comp.4
SS loadings      1.00   1.00   1.00   1.00
Proportion Var   0.25   0.25   0.25   0.25
Cumulative Var   0.25   0.50   0.75   1.00

levels(penguins2$species)
[1] "Adelie"    "Chinstrap" "Gentoo"   

To get PCA scores

penguin_pca$scores
            Comp.1       Comp.2        Comp.3       Comp.4
  [1,] -1.85359302  0.032069377 -0.2349016613  0.528396625
  [2,] -1.31625406 -0.443526765 -0.0274700760  0.401726631
  [3,] -1.37660509 -0.161230478  0.1896892637 -0.528661902
  [4,] -1.88528838 -0.012351235 -0.6288726870 -0.472893203
  [5,] -1.91998074  0.817598126 -0.7010513885 -0.196416463
  [6,] -1.77302031 -0.366222957  0.0284604590  0.505368579
  [7,] -0.81849625  0.501243084 -1.3350037341  0.348259556
  [8,] -1.79895773 -0.245393945  0.6265541188  0.215177636
  [9,] -1.95614892  0.998282895 -1.0406150295 -0.210615154
 [10,] -1.56952316  0.578081948 -2.0492974540 -0.263635364
 [11,] -1.74800122 -0.610244291 -0.3648455682  0.275254393
 [12,] -1.57577371  0.086835726 -0.3623210792 -0.507079122
 [13,] -0.80472019  1.293555921 -1.0898644424  0.107519267
 [14,] -2.35017809 -0.645191072 -0.4607707684 -0.048857069
 [15,] -1.00498645  1.972422509 -0.5798770729  0.084976671
 [16,] -2.40824844 -0.308968645  0.0744441020  0.662978776
 [17,] -2.11369825 -0.136493144 -0.2723621056  0.437971409
 [18,] -1.85705729 -0.109144060 -0.8914621801 -0.007995218
 [19,] -1.50501042 -0.289127997 -0.4255462669  0.475198437
 [20,] -1.58113786 -0.603932517  0.0346978179  0.734644053
 [21,] -1.92846722 -0.297394981 -0.8633540656  0.112204664
 [22,] -1.76295054  0.138259762  0.0767052076  0.319209942
 [23,] -1.70361341 -0.187802307  0.4066389913 -0.104556344
 [24,] -2.71417458 -0.201106317  0.2389821840  0.571190457
 [25,] -1.68232816  0.285542330 -0.2438102280  0.750672188
 [26,] -1.87994963 -0.782580998  0.6638711756  0.505701001
 [27,] -1.91081367 -0.406695073 -0.3883180768  0.803391776
 [28,] -1.65683258 -0.328286332  0.2201618206 -0.106165116
 [29,] -1.51840291  0.326408242 -0.2274268406  0.501437178
 [30,] -1.44646684 -0.987685263 -0.1078452205 -0.496481192
 [31,] -1.44062410  1.059095864 -1.2903086836 -0.211391293
 [32,] -1.63466140  0.548223391 -0.8507480012  0.057249680
 [33,] -1.73335112  0.272394506  0.3372327369  0.537510640
 [34,] -2.40765908  0.067345151 -0.2101338390  0.112476774
 [35,] -1.13764744  0.357809820 -0.9521566896  1.001340496
 [36,] -2.29657080 -0.593801144  0.0354812471  0.023993523
 [37,] -0.97184877  0.117509989 -0.3164908762 -0.075207890
 [38,] -2.30890668 -0.449404139 -0.1623082340 -0.289830288
 [39,] -0.57840195  1.054586456 -0.5945824193  0.214535227
 [40,] -2.01067992 -0.997271019  0.3923067603 -0.149971631
 [41,] -0.88026262  0.212079200 -0.9751464709  0.648796919
 [42,] -1.92925587  0.342881528  0.1577848524  0.264948453
 [43,] -1.78298528 -0.657410953 -0.3574537623 -0.210018964
 [44,] -1.40940140  1.438260966 -0.8628557816  0.142277387
 [45,] -1.57392895 -0.339592411  0.1401266848  0.161823273
 [46,] -1.14654389  0.278170592 -0.6834333861  0.547546732
 [47,] -1.86608339 -0.767327681 -0.4751171379 -0.236604598
 [48,] -0.78673386  0.711147080 -0.6082512171 -0.303064057
 [49,] -2.44789222 -0.794851225 -0.1218556728 -0.498499722
 [50,] -1.26418254  0.243767425 -0.0745246189  0.002543992
 [51,] -1.54901519 -0.481769739  0.0760396714  0.198497399
 [52,] -1.22044841  0.247154032 -0.3193049336 -0.074021804
 [53,] -2.25876529 -1.189622965  0.5763198147 -0.024441402
 [54,] -1.52359256  0.034535966 -0.7173315591 -0.270413670
 [55,] -2.01615696 -1.125897262  0.1289464113 -0.075450514
 [56,] -1.13641794  1.313283236 -1.2103418754  0.082119719
 [57,] -1.57091360 -0.833767737 -0.0003422234  0.294177168
 [58,] -0.92743183  0.082527261 -0.2976685297  0.225746271
 [59,] -2.24489579 -0.996917698  0.4056666843 -0.235393033
 [60,] -0.91366065  0.046992829 -0.1219278693  0.182582152
 [61,] -1.34180687 -1.408162573 -0.0589005898 -0.437169086
 [62,] -1.24076891  0.450049108 -0.4618830617  0.412424419
 [63,] -1.80093377 -1.232829956  0.2066916214 -0.397843538
 [64,] -0.59202566  0.685886654 -0.8707826466  0.102391897
 [65,] -2.11142026 -0.472533742 -1.0002169890 -0.256856415
 [66,] -1.26934357 -0.005466398 -0.3615689854  0.174933474
 [67,] -1.02609887 -0.533157420  0.0428999873 -0.319925306
 [68,] -0.40447877  0.894152813 -0.0541870716  0.087108392
 [69,] -1.57243857 -0.850558396 -0.5136613869 -0.008978328
 [70,] -0.58666260  0.411120851 -0.3604145329  0.224356728
 [71,] -0.94042944 -0.540033074  0.2564366830  0.135633405
 [72,] -1.92733875  0.122172496 -0.7710571606  0.362408603
 [73,] -1.45634863 -1.356000198  0.0328842243  0.182033357
 [74,] -0.93751617  0.553350680 -0.3887132911 -0.024851361
 [75,] -1.96939557 -1.118922417 -0.1697294034 -0.316239385
 [76,] -0.04683282  0.100901565 -0.5018159035  0.571576618
 [77,] -1.79183530 -0.184002791 -0.6769701737  0.157556898
 [78,] -1.52578740 -0.076399251 -1.3907790578  0.021849643
 [79,] -1.68181280 -0.564107174 -0.1261078882 -0.295924034
 [80,] -1.59639832  0.908101945 -0.3946417816 -0.415078234
 [81,] -1.84348437  0.056709917 -0.9262326489 -0.077635115
 [82,] -1.85729280 -0.270705718 -0.4230718864 -0.150780390
 [83,] -1.55507132  0.168921592 -0.7194680394  0.164892744
 [84,] -1.62210133  0.040034131 -0.3215244287 -0.097029300
 [85,] -1.26523377 -0.635421240 -0.6904504308 -0.823930721
 [86,] -0.20039388  0.071188634 -0.6793241349 -0.310719775
 [87,] -2.02709537 -1.207997401 -0.2983882606  0.044893285
 [88,] -1.00562068 -0.087279300 -0.6456810644  0.820149350
 [89,] -1.87080090 -0.893881281 -0.0429811675 -0.097358865
 [90,] -0.26402770  0.363384244 -0.9384754387 -0.551385571
 [91,] -1.57962369 -0.119371375 -0.4459434375 -0.029311487
 [92,] -0.68482350  0.146252964 -0.7450419331  0.174737159
 [93,] -2.52929467 -1.762281613  0.2983518103  0.129821325
 [94,] -0.77962599  0.439581247 -0.1523402596  0.293539877
 [95,] -1.59563939 -0.740347063 -0.7112540408 -0.148374347
 [96,] -0.38617540  0.869122059 -1.3815922089 -0.047071773
 [97,] -1.80101966 -1.278444819  0.6481092793  0.108124873
 [98,] -1.51265850  0.466837670 -1.1892072983  0.248828929
 [99,] -2.00243546 -0.213819033  0.0503023889 -0.765852564
[100,] -1.85740516  0.161221992 -0.1110276495  0.215008721
[101,] -0.84881085 -0.622812685 -0.2725716316 -0.368699022
[102,] -1.71870377  0.477518186 -0.8845467063  0.004937486
[103,] -1.98479380 -0.820882689  0.4387649696  0.221911517
[104,] -0.21353466  0.708300149 -0.8417585173  0.464363571
[105,] -0.73824008 -0.954490503 -0.2181458163 -0.214647083
[106,] -0.64487503  1.479361613 -0.6108640296  0.630448418
[107,] -1.48219852 -0.354236566  0.2545966984 -0.444822833
[108,] -0.73994061  0.753287890 -0.6997045208  0.033508069
[109,] -1.70321099  0.915253811 -0.8882744639 -0.070646162
[110,] -0.63280816  0.302917228 -0.2169432381  0.054822896
[111,] -1.84273238 -0.789182569  0.5819006733 -0.355919928
[112,] -1.60946727  0.572883733 -1.1585541611 -0.653447361
[113,] -1.73484802 -1.064730972 -0.1073873188 -0.161648054
[114,] -1.62792299  0.174301453  0.1999119118 -0.166383577
[115,] -1.95305685 -0.948638014  0.0890719593 -0.198308960
[116,] -1.66339271  0.306844796 -0.7406360661 -0.729994048
[117,] -1.82836539 -0.565972121  0.5678134008  0.757111386
[118,] -0.67085459  0.224468852 -0.3672406022 -0.476709049
[119,] -1.88191000 -1.594864662  0.3433947042 -0.136018610
[120,] -0.87699928  0.349638746 -0.6110344714 -0.280105915
[121,] -1.56785175 -0.487347294  0.1488964877 -0.294322112
[122,] -0.61991752  0.192001813 -0.5068659092  0.242420910
[123,] -1.60358507 -0.689218352  0.4463019344 -0.411966916
[124,]  0.07018089  0.333984567 -0.1682345245 -0.720380972
[125,] -1.66069875 -0.394507052  0.0287029773 -0.234456914
[126,] -1.13411289  0.657034153  0.0415474793 -0.481760436
[127,] -1.68043855 -0.320534232 -0.4806643410 -0.368815057
[128,] -0.70838734 -0.148385164 -1.2171086476  0.023568081
[129,] -1.68833943 -0.551677888  0.0236154471  0.019658835
[130,] -0.97035514 -0.216004046 -0.0019437648  0.285344477
[131,] -1.88183815 -0.889082390 -0.1323725075 -0.443985421
[132,] -1.10935310  0.749111595 -0.8947773093 -0.454253495
[133,] -1.65603365 -1.121194594  0.1845328627  0.173444263
[134,] -0.80493412 -0.173395579 -0.5614993590  0.302489564
[135,] -1.18214807 -0.523204908  0.2961621018 -0.237292684
[136,] -1.36523239 -0.434095818  0.3675952302  0.155013118
[137,] -1.97590114 -2.096744245  0.0315182628 -0.297658915
[138,] -1.02176382 -0.479069974  0.1880643363  0.188109106
[139,] -1.67693429 -1.001892051  0.3311686937 -0.525003382
[140,] -1.76540033  0.013221756 -0.2405506415  0.229507985
[141,] -1.11219725  0.053843874 -0.7213062471  0.399901662
[142,] -2.06481174 -0.389108766 -0.3123093029  0.118713766
[143,] -1.55660384 -0.695834197 -0.4201502001 -0.481272180
[144,] -1.34524467 -0.348806583 -0.4603769023 -0.127895970
[145,] -1.57336339 -0.958805742 -0.3175980725  0.204475211
[146,] -0.61830340  0.246934847 -0.4306022445 -0.327271339
[147,]  1.59356859 -1.341795728  0.7216766759  0.030873935
[148,]  2.89205390  0.464090012 -0.6944660890 -0.306550426
[149,]  1.55157173 -0.696759932  0.8863745985  0.046321767
[150,]  2.62068561  0.013723319 -0.2538154127  0.453430729
[151,]  2.23455895 -0.563287236 -0.1132144676  0.396018085
[152,]  1.55889027 -1.172013776  0.6838475283  0.109349077
[153,]  1.45637702 -0.823329213  0.1153440662  0.116576029
[154,]  2.02554963 -0.355648737 -0.3126368365 -0.061919459
[155,]  1.16950299 -1.578917638  0.4562481741 -0.020797935
[156,]  1.81451188 -0.310575391 -0.2182450616  0.119754394
[157,]  1.28618821 -1.695400271 -0.1594576306 -0.206581987
[158,]  2.16995116  0.253134960 -0.4222366808  0.356325763
[159,]  1.66843953 -1.189783321  0.3817938970 -0.084288071
[160,]  2.50595964 -0.392893307 -0.3381921739  0.848155795
[161,]  1.03819687 -0.836838135  0.6208715802 -0.253242371
[162,]  2.52237724  0.153089665 -0.5379832461  0.559118608
[163,]  0.91148075 -1.704680397  0.4487569003 -0.301172786
[164,]  3.08806126 -0.015907257 -0.8401489185  0.700860650
[165,]  1.46071532 -0.776714255  0.2648705743  0.257731106
[166,]  2.45853762 -0.201291445 -0.1950086762 -0.051032395
[167,]  2.81995631 -0.328714403 -0.0353862428  0.531938971
[168,]  1.75334566 -0.876120401 -0.1129783445  0.038667490
[169,]  1.37704625 -0.780126191  0.5270828658 -0.248688163
[170,]  1.62341756 -0.213079172 -0.2900987733  0.001210565
[171,]  1.85465371 -1.684814420 -0.0686654454  0.094031942
[172,]  1.78304339 -0.513745958 -0.1988446060  0.089180675
[173,]  2.32062326 -0.315071902 -0.3819542242  0.542477550
[174,]  1.57198405 -0.656470332  0.6738346178  0.125846699
[175,]  2.58027529  0.040776239 -0.1988132596  0.224461717
[176,]  2.23324413 -0.283702741 -0.3294490937 -0.177238602
[177,]  1.17069843 -1.281415156  0.0033792361  0.119015362
[178,]  1.45779016 -0.874674010 -0.0148150986  0.522045203
[179,]  3.78701834  1.836015387  0.0259209120  0.146270932
[180,]  2.33349180 -0.298646309  0.0979600949 -0.049690133
[181,]  2.14182216  0.255556267 -0.4932283607 -0.008481200
[182,]  1.59133864 -1.480424422 -0.1633554929  0.112655586
[183,]  1.46271619  0.206122550 -1.0531652424 -0.249352525
[184,]  1.11168166 -1.426162233  0.5489718459  0.001063615
[185,]  1.75972697  0.035865574 -0.0887551819  0.682453101
[186,]  0.70989154 -1.566604094  0.6687488536 -0.332516565
[187,]  2.71361148  0.296581645 -0.5922143371 -0.013402080
[188,]  1.24766590 -1.246707231  0.6833377467 -0.120622445
[189,]  1.89611421 -0.202401218  0.4753572955 -0.120040069
[190,]  2.58249171  0.339509176 -0.3036532099  0.077206232
[191,]  1.76453362 -1.292626014 -0.1196844123 -0.136892736
[192,]  1.15532939 -1.153251761  0.7371587302 -0.204291638
[193,]  2.60359333  0.326484463 -0.2438662115 -0.199507546
[194,]  1.96619306 -1.375315362  0.0834929746  0.315414369
[195,]  1.70292714 -0.310211734 -0.6035250877  0.153770437
[196,]  1.63023914 -0.849052487  0.3232317817  0.273246100
[197,]  2.52824538 -0.633769450  0.0685502714  0.100367351
[198,]  1.15735133 -0.975741632  0.4346202685 -0.110144367
[199,]  2.47953715 -0.119944640  0.1983594951 -0.427837195
[200,]  1.90404533 -0.771411353  0.1132635463 -0.100456128
[201,]  1.80265515 -0.515867852 -0.4407921010 -0.280206936
[202,]  0.99999485 -1.331427058  0.4972729927 -0.065011363
[203,]  1.89119896 -0.627629575 -0.2585404286 -0.270745548
[204,]  0.93091910 -1.140164212  0.1863460101 -0.020674379
[205,]  2.77838403  0.086397319 -0.2192291925  0.011587521
[206,]  1.07656958 -1.216553531  0.7690218627 -0.089722194
[207,]  2.21598059 -0.562234490 -0.3921871419 -0.081715488
[208,]  1.47355252 -1.110593355  0.5460128412 -0.277039706
[209,]  3.37817705  0.689442994 -0.0386535780 -0.235676050
[210,]  1.83216652 -0.947529000  0.1876661551 -0.359998860
[211,]  2.77396146  0.644562815 -0.8262745946 -0.352529284
[212,]  2.89794904  0.377737157 -0.7883709304 -0.183112157
[213,]  1.68225824 -1.199923878 -0.0998299295 -0.477022930
[214,]  2.82297979 -0.002514949 -0.1020943607  0.099837362
[215,]  1.73822780 -0.411243001  0.2517968820 -0.170552774
[216,]  1.88543725 -0.285343544 -0.2994447079 -0.351489667
[217,]  2.10338085 -0.077983097 -0.1612492724 -0.230913899
[218,]  2.02796808 -0.580915426 -0.1941530395  0.085179370
[219,]  1.59601675 -0.558889916  0.1356338140 -0.241474911
[220,]  2.90496724  0.198243239 -0.8678279570 -0.246651648
[221,]  1.49289256 -0.774316869  0.6299957418  0.171246214
[222,]  2.77638908  0.609393449 -0.6171290897  0.499629777
[223,]  1.73279991 -1.172343176  0.2343707570 -0.083551592
[224,]  2.35528428 -0.002138394 -1.3468098137  0.130650040
[225,]  1.70570972 -0.473358039  0.6842810220  0.039935259
[226,]  2.69998725  0.427945010  0.0871080008  0.137930023
[227,]  1.61251537 -0.610214911  0.3889994769  0.059328963
[228,]  2.48664340  0.266357334 -0.2490282583 -0.193284064
[229,]  1.58421835 -1.206558986  0.2496827066  0.076104055
[230,]  2.60478500  0.946598161 -0.7095477675 -0.327572783
[231,]  1.48255754 -1.140270621 -0.0475673172 -0.456913588
[232,]  2.65819078 -0.286338576  0.4100931985  0.278429004
[233,]  1.84514307 -0.827905113  0.4202988503  0.219864045
[234,]  2.82194749  0.964088245 -0.4885612022 -0.416729460
[235,]  1.94077693 -0.413378481  0.0473262843 -0.142180870
[236,]  2.62497748  1.000478450 -0.3543114285 -0.419531459
[237,]  1.49201527 -0.857170341  0.1686945693  0.035129012
[238,]  2.60960622  0.320912437 -0.5719661997 -0.004676691
[239,]  1.51912978 -0.875767080 -0.0996184205 -0.046753911
[240,]  2.57359526  0.259869947 -0.0349299064 -0.376587531
[241,]  1.83678033  0.116188362  0.1497856708 -0.063153117
[242,]  2.08569057 -0.646771800  0.0510666206 -0.403652536
[243,]  1.29687923 -0.594513353  0.7754047121  0.532351673
[244,]  2.42913431  0.621116375 -0.1928012220 -0.341432684
[245,]  1.99672542 -0.312558491  0.2217179796 -0.244193976
[246,]  3.08946906  1.385699786 -0.0444990538 -0.167589013
[247,]  1.70781430 -0.242760558 -0.0640372566 -0.005006547
[248,]  2.86192618 -0.181068897 -0.3379080453 -0.258446028
[249,]  1.91173444  0.006149393 -0.6274264661  0.317353668
[250,]  1.01903506 -1.199453811 -0.2511966283 -0.006767678
 [ reached getOption("max.print") -- omitted 83 rows ]

ADD LESSON STUFF FROM LAST CLASS

Statistics

Additional Ways of Importing, Reading, and Manipulating Data

Hard method:

rand
[1] 12 54 98 65 38

To get cumulative sum:

sum(rand)
[1] 267
length(rand)
[1] 5

To get the mean of your data:

avg.rand
[1] 53.4

Another way to get the average:

mean(rand)
[1] 53.4

To sort:

sort(rand)
[1] 12 38 54 65 98
min(rand)
[1] 12
max(rand)
[1] 98
cumsum(rand)
[1]  12  66 164 229 267

To get differences:

diff(rand)
[1]  42  44 -33 -27

Slicing/Indexing #’s out:

rand[2]
[1] 54

Transforming #’s: adding, multiplying, etc

Importing Data, Most Useful: Take a list of numbers, don’t need to add comma’s and just paste in data. Press ‘enter’ twice to finish adding data

peds
 [1]  2  3 16 23 14 12  4 13  2  0  0  0  6 28 31 14  4  8  2  5

Analyses

Univariate Statistics

1. Categotical Data
a. Barplots
length(beer)
[1] 25

You cannot use “barplot(beer)” command right away. It will just show you every # in its own column

table(beer)
beer
 1  2  3  4 
10  4  8  3 

This is just for counts/frequency:

For proportion:

b. Pie Charts

2. Numerical Data
a. Stem-and-Leaf Plots
stem(peds)

  The decimal point is 1 digit(s) to the right of the |

  0 | 000222344568
  1 | 23446
  2 | 38
  3 | 1
b. Strip Chart

3. Measures of Center
a. Mean
mean(peds)
[1] 9.35

Using Columns in Data frame:

mean(gapminder2$lifeExp)
[1] 59.47444
b. Median
median(peds)
[1] 5.5
median(gapminder2$lifeExp)
[1] 60.7125

Must know exact column headers using the “with” command

with(gapminder2, median(lifeExp))
[1] 60.7125
c. Mode

Frequency of measurement occurring:

which(table(peds) == max(table(peds)))
0 2 
1 2 
4. Variation/Spread
a. Range
range(peds)
[1]  0 31

Will give you a summary of the range:

diff(range(peds))
[1] 31
b. Variance
var(peds)
[1] 87.60789

Standard Deviation: sqrt of variance

sd(peds)
[1] 9.359909
c. Inter-quartile Range (IQR)
IQR(peds)
[1] 12
d. Z-Scores

The number of standard deviations away from the mean

scale(peds)
            [,1]
 [1,] -0.7852641
 [2,] -0.6784254
 [3,]  0.7104770
 [4,]  1.4583475
 [5,]  0.4967997
 [6,]  0.2831224
 [7,] -0.5715868
 [8,]  0.3899611
 [9,] -0.7852641
[10,] -0.9989413
[11,] -0.9989413
[12,] -0.9989413
[13,] -0.3579095
[14,]  1.9925408
[15,]  2.3130567
[16,]  0.4967997
[17,] -0.5715868
[18,] -0.1442322
[19,] -0.7852641
[20,] -0.4647481
attr(,"scaled:center")
[1] 9.35
attr(,"scaled:scale")
[1] 9.359909
e. Summaries
summary(peds)
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
   0.00    2.00    5.50    9.35   14.00   31.00 
5. Plotting
a. Histogram

Modify # of breaks:

hist(peds, breaks="scott", prob=TRUE)
lines(density(peds))

b. Boxplots

Bivariate & Multivariate Statistics

1. Plotting & Regression
a. Boxplotting
boxplot(spid.gen)
Error in x[floor(d)] + x[ceiling(d)] : 
  non-numeric argument to binary operator

b. Scatterplots

Changing plot characters using pch

c. Linear Regression

To use a linear model, define general regression variable using lm():

gen.reg <- lm(spid.gen$left.bulb ~ spid.gen$right.bulb)
gen.reg

Call:
lm(formula = spid.gen$left.bulb ~ spid.gen$right.bulb)

Coefficients:
        (Intercept)  spid.gen$right.bulb  
            47.2805               0.7545  

Using summary(gen.reg) will result in an ANOVA test:

summary(gen.reg)

Call:
lm(formula = spid.gen$left.bulb ~ spid.gen$right.bulb)

Residuals:
    Min      1Q  Median      3Q     Max 
-28.973 -16.272  -7.931  12.167  48.620 

Coefficients:
                    Estimate Std. Error t value Pr(>|t|)   
(Intercept)          47.2805    27.0506   1.748  0.10600   
spid.gen$right.bulb   0.7545     0.1974   3.823  0.00243 **
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

Residual standard error: 24.67 on 12 degrees of freedom
Multiple R-squared:  0.5491,    Adjusted R-squared:  0.5115 
F-statistic: 14.61 on 1 and 12 DF,  p-value: 0.002427

Using abline will give you your linear regression line into your plot:

plot(spid.gen$left.bulb ~ spid.gen$right.bulb, pch = as.character(spid.gen$habitat))
abline(gen.reg)

d. Correlation Coefficient & Spearman Rank Correlation

Cor.gen will give you your R-value, to get R^2, use cor.gen^2:

cor.gen <- with(spid.gen, cor(left.bulb, right.bulb))
cor.gen
[1] 0.7410186
cor.gen^2
[1] 0.5491086
spearman.cor.gen^2
[1] 0.5274774
e. Residuals

Residuals are the difference between a value and the line of best fit (LOBF)

residuals(gen.reg)
         1          2          3          4          5          6          7          8          9         10         11         12         13         14 
  9.026729 -17.942400  21.026729 -10.116375 -21.410662 -28.973271  -5.901718  48.620209 -11.259480  -2.241592  40.566544  13.213688 -24.648113  -9.960288 
f. Transformations

log.left.bulb <- log10(spid.gen$left.bulb)
2. Comparing Descrete Treatment Effects
a. Chi-Squared Test
chisq.test(obs, p=exp)

    Chi-squared test for given probabilities

data:  obs
X-squared = 21.691, df = 5, p-value = 0.0005993
obs_weighted <- c(4,15,6,15,18,2)
obs_fair <- c(10,10,10,10,10,10)
exp <- c(0.16,0.17,0.16,0.17,0.17,0.17)

This will be significant:

chisq.test(obs_weighted, p=exp)

    Chi-squared test for given probabilities

data:  obs_weighted
X-squared = 21.691, df = 5, p-value = 0.0005993

This is not significant since p=value is 1:

chisq.test(obs_fair, p=exp)

    Chi-squared test for given probabilities

data:  obs_fair
X-squared = 0.04902, df = 5, p-value = 1
b. T-test

Null hypothesis (H0): true mean is equal to zero, but you can set true mean to other values with “mu=”

1 Sample T-Test: Student T-Test (2-Tail Test)

t.test(spid.gen$carapace.length)

    One Sample t-test

data:  spid.gen$carapace.length
t = 27.953, df = 13, p-value = 5.373e-13
alternative hypothesis: true mean is not equal to 0
95 percent confidence interval:
 26.69279 31.16436
sample estimates:
mean of x 
 28.92857 
mean(spid.gen$carapace.length)
[1] 28.92857
t.test(spid.gen$carapace.length, mu=29)

    One Sample t-test

data:  spid.gen$carapace.length
t = -0.069019, df = 13, p-value = 0.946
alternative hypothesis: true mean is not equal to 29
95 percent confidence interval:
 26.69279 31.16436
sample estimates:
mean of x 
 28.92857 

2 Sample T-Test:

habitat.t2

    Welch Two Sample t-test

data:  spid.gen$left.bulb by spid.gen$habitat
t = -4.9442, df = 11.485, p-value = 0.0003868
alternative hypothesis: true difference in means between group A and group B is not equal to 0
95 percent confidence interval:
 -80.38903 -31.03954
sample estimates:
mean in group A mean in group B 
       119.7143        175.4286 
habitat.t2 <- t.test(spid.gen$left.bulb~spid.gen$habitat)
habitat.t2

    Welch Two Sample t-test

data:  spid.gen$left.bulb by spid.gen$habitat
t = -4.9442, df = 11.485, p-value = 0.0003868
alternative hypothesis: true difference in means between group A and group B is not equal to 0
95 percent confidence interval:
 -80.38903 -31.03954
sample estimates:
mean in group A mean in group B 
       119.7143        175.4286 

1 Sample Test: Is one less than the other? (1-Tailed)

habitat.tless

    One Sample t-test

data:  spid.gen$left.bulb
t = 15.643, df = 13, p-value = 1
alternative hypothesis: true mean is less than 0
95 percent confidence interval:
     -Inf 164.2781
sample estimates:
mean of x 
 147.5714 

Conclusion: B is not less than A

1 Sample Test: Is one greater than the other? (1-Tailed)

habitat.tgreater <- t.test(spid.gen$left.bulb, alternative = "greater")
habitat.tgreater

    One Sample t-test

data:  spid.gen$left.bulb
t = 15.643, df = 13, p-value = 4.109e-10
alternative hypothesis: true mean is greater than 0
95 percent confidence interval:
 130.8648      Inf
sample estimates:
mean of x 
 147.5714 
c. Analysis Of Variance (ANOVA)
gen.lm

Call:
lm(formula = spid.gen$left.bulb ~ spid.gen$habitat)

Coefficients:
      (Intercept)  spid.gen$habitatB  
           119.71              55.71  
summary(gen.lm)

Call:
lm(formula = spid.gen$left.bulb ~ spid.gen$habitat)

Residuals:
    Min      1Q  Median      3Q     Max 
-29.714 -16.250   2.429  20.036  23.286 

Coefficients:
                  Estimate Std. Error t value Pr(>|t|)    
(Intercept)        119.714      7.968  15.024 3.82e-09 ***
spid.gen$habitatB   55.714     11.269   4.944  0.00034 ***
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

Residual standard error: 21.08 on 12 degrees of freedom
Multiple R-squared:  0.6707,    Adjusted R-squared:  0.6433 
F-statistic: 24.45 on 1 and 12 DF,  p-value: 0.0003397
anova(gen.lm)
Analysis of Variance Table

Response: spid.gen$left.bulb
                 Df  Sum Sq Mean Sq F value    Pr(>F)    
spid.gen$habitat  1 10864.3 10864.3  24.445 0.0003397 ***
Residuals        12  5333.1   444.4                      
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
gen.anova
Call:
   aov(formula = spid.gen$left.bulb ~ spid.gen$habitat)

Terms:
                spid.gen$habitat Residuals
Sum of Squares         10864.286  5333.143
Deg. of Freedom                1        12

Residual standard error: 21.08147
Estimated effects may be unbalanced
summary(gen.anova)
                 Df Sum Sq Mean Sq F value  Pr(>F)    
spid.gen$habitat  1  10864   10864   24.45 0.00034 ***
Residuals        12   5333     444                    
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

Note: You get the same output

summary(gapminder2.lifeexp.continent.anova)
                       Df Sum Sq Mean Sq F value Pr(>F)    
gapminder2$continent    4 139343   34836   408.7 <2e-16 ***
Residuals            1699 144805      85                   
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

Performing a Post Hoc Test: Tukey Test

gapminder2.tukey.two.way <- TukeyHSD(gapminder2.lifeexp.continent.anova)
gapminder2.tukey.two.way
d. Analysis of Covariance (ANCOVA)

Supplying to model other factors that might explain the differences

boxplot(spid.gen$left.bulb~spid.gen$habitat)

Use a covariate by adding *factor_you_want_to_control

gen.ancova <- lm(spid.gen$left.bulb~spid.gen$habitat*spid.gen$carapace.length)
summary(gen.ancova)
gapminder2.lifeexp.continent_GDP.ancova <- aov(gapminder2$lifeExp~gapminder2$continent+gapminder2$gdpPercap)
summary(gapminder2.lifeexp.continent_GDP.ancova)
install.packages("multcomp")
library(multcomp)
#posthoc.gapminder2.ancova <- glht(gapminder2.lifeexp.continent_GDP.ancova, linfct=mcp(technique="Tukey")) (isn't working)
3. Principle Component Analysis
sp.matrix <- with(spid.gen, cbind(left.bulb, right.bulb, carapace.length, leg4.length))
sp.matrix
sp.pca <- princomp(sp.matrix, cor=TRUE)
summary(sp.pca)
loadings(sp.pca)
biplot(sp.pca)
install.packages("ggfortify", dependencies = TRUE)
sp.pca$scores
library(ggfortify)

Plot Cheatsheet

plot(1:25, rep(0.25,25), pch=1:25, col=1:25, ylim=c(0,6), cex=2, ylab="Line types (lty) 1 to 6", xlab="Plotting character (pch) 1 to 25 and colours (col) 1 to 8", main="Line types (lty), plotting characters (pch),\nand colors (col) for plot and xyplot", lab=c(25,7,2))

points(1:8, rep(0.5,8), pch=20, col=1:8, cex=4)

abline(h=1:6, lty=1:6, lwd=5, col=1:8)

Looping and Conditionals

A. If-Then Statements

x <- 5
if(x > 0){
  print("Positive #")}
[1] "Positive #"
x <- -5
if(x > 0){
  print("Positive #")
} else if (x < 0) {
  print("Negative #")
} else
  print("Zero")

%% Represents division, and == means no remainder “if its true”, “if its odd”

a <- c(5,7,2,9)
ifelse(a %% 2 == 0, "even", "odd")
[1] "odd"  "odd"  "even" "odd" 

B. For Loops

For each of these values in Z, divide them by 2, if they don’t have a remainder, it will tell you how many even numbers

z <- c(2,5,3,9,8,11,6)
count <- 0

for(val in z) {
  if(val %% 2 == 0) count = count + 1
}
  print(count)
[1] 3

C. While Statement

while (i < 5) {
  print(i)
  i = i +1
}
[1] 1
[1] 2
[1] 3
[1] 4

D. Interruptions

Breaks the loop

x <- 1:5
for (val in x){
  if (val == 3){
    break
  }
  print(val)
}
[1] 1
[1] 2

If print(val) is placed before the break, it will print the value 3, then break the loop

x <- 1:5
for (val in x){
  if (val == 3){
    print(val)
    break
  }
  #print(val)
}
[1] 3
x <- 1:5
for (val in x){
  print(val)
  if (val == 3){
    #print(val)
    break
  }
  #print(val)
}
[1] 1
[1] 2
[1] 3

If the value is equal to 3, it will skip that value and move onto the next one

for (val in x){
  if (val == 3) {
    next
  }
  print(val)
}
[1] 1
[1] 2
[1] 4
[1] 5
x <- 1
repeat{
  print(x)
  x = x+1
  if (x == 20) {
    break
  }
}
[1] 1
[1] 2
[1] 3
[1] 4
[1] 5
[1] 6
[1] 7
[1] 8
[1] 9
[1] 10
[1] 11
[1] 12
[1] 13
[1] 14
[1] 15
[1] 16
[1] 17
[1] 18
[1] 19

Randomization & Dataset Management (short)

A. Dataset Management

matrix_B
     [,1] [,2]
[1,]    2    1
[2,]    4    5
[3,]    3    7

Transforming Data

t(matrix_B)
     [,1] [,2] [,3]
[1,]    2    4    3
[2,]    1    5    7
matrix_C <- matrix(
  c(7,4,2),
  nrow=3,
  ncol=1
)

matrix_C
     [,1]
[1,]    7
[2,]    4
[3,]    2

Putting the Matrices/Data.frame together

matrix_BC
     [,1] [,2] [,3]
[1,]    2    1    7
[2,]    4    5    4
[3,]    3    7    2

Deconstructing the Matrices

c(matrix_BC)
[1] 2 4 3 1 5 7 7 4 2

B. Randomizations

Each tiime you run the script, you will get different numbers

rnorm(# samples, average, variance as standard deviation) sample(what you want to sample, size of sample, replace = FALSE, prob = NULL)

ndist 
  [1]  55.9542490  26.3697544  89.4133606  30.4705159  77.4904339  45.1497019  42.5528411  55.8054149  66.2090974
 [10]  81.9794886  58.9407723  54.2343070  54.3273391  33.0817729  75.3197815  26.2599278  70.6045629  38.6222709
 [19]   0.8912044   3.9895768  68.4496573  75.7090393  69.6527897   0.4292658  18.1040327  32.2248827  45.7944139
 [28]  65.8302703  85.7585557  31.2537956  18.9440611  54.0444611  44.9547697  37.9902935  71.7696526  70.4014492
 [37]  40.9347399  62.3939766  65.3758079  42.6461025  50.0646070  76.2433791  29.1494626  24.2207133  51.3884549
 [46]  35.1167009  42.0008419  56.9603999  72.9600210  57.1145944  89.9174185  35.6649101  39.9447309  24.8010554
 [55]  54.4779804  89.6292238  67.3184735  40.5109672  64.2697703  60.9038885  73.4688038  52.7006923  -2.0313551
 [64]  23.9281731  60.7924906  46.2207658  60.4088549  34.5986970  62.5923770 109.2151936  47.8052044  10.5844283
 [73]  38.7855412  81.5907308  37.6361760  45.7837776  64.5194886  29.2113467  69.6984450  46.8443136  64.7202652
 [82]  62.6272938  65.9904559  31.4220989  56.3600481  92.1638530  59.7632149  40.3388356   6.6850950  31.8363553
 [91]  50.8770143  56.6747157  47.7469551 110.4550490  42.0540827  47.5342241  48.4177596  44.9337455  69.7509705
[100]  51.5046615

sample(ndist, 10, replace = FALSE, prob = NULL)
 [1] 92.163853 33.081773 64.519489 67.318474  6.685095 65.375808 32.224883 42.552841 56.360048 50.877014

Sampling With & Without Replacement

test <- 1:100
test
  [1]   1   2   3   4   5   6   7   8   9  10  11  12  13  14  15  16  17  18  19  20  21  22  23  24  25  26  27  28  29
 [30]  30  31  32  33  34  35  36  37  38  39  40  41  42  43  44  45  46  47  48  49  50  51  52  53  54  55  56  57  58
 [59]  59  60  61  62  63  64  65  66  67  68  69  70  71  72  73  74  75  76  77  78  79  80  81  82  83  84  85  86  87
 [88]  88  89  90  91  92  93  94  95  96  97  98  99 100

No repeats:

sort(sample(test, 50, replace = FALSE, prob = NULL))
 [1]   1   2   3   4   6   9  10  11  14  16  20  21  22  23  24  25  27  30  32  34  36  38  40  43  44  52  54  62  65
[30]  67  68  72  73  74  75  78  80  83  85  86  88  91  92  94  95  96  97  98  99 100

Now you can have repeats:

sort(sample(test, 50, replace = TRUE, prob = NULL))
 [1]   1   3   8  11  13  21  22  27  29  30  31  31  37  37  38  42  44  47  53  57  57  59  59  60  61  64  66  66  68
[30]  69  69  70  72  73  74  74  76  78  79  79  83  84  88  90  91  91  92  96  97 100
---
title: "R_Studio_Tutorial"
output:
  html_notebook: default
  pdf_document: default
  html_document:
    df_print: paged
---
# R Basics

## Introduction

To enter code use command+enter

### R Calculator

Basic calculations:
```{r}
1+100
```

```{r}
2^2
```

```{r}
7/2
```
```{r}
10-2
```

```{r}
2*2
```

Order of operations matter: PEMDAS
```{r}
3+5*2
(3+5)*2
```

Using scientific notation:
```{r}
2e2
2/10000
```

Can also use trigometric functions:
```{r}
log(1)
exp(0)
```


You can also ask questions: T/F Statements
```{r}
1 == 1

1 >=1

1 < 1

1 != 2
```

You can define objects/variables:
```{r}
x <- 10
x
x+x
```

```{r}
y <- x+x
y
```

### Vectorization

Use the colon *:* to make a list:
```{r}
1:5
```

Conducting operations on vectors:
```{r}
2^(1:5)
```

Storing vector as an object:
```{r}
v <- 1:5
2^v
```

Log transformations:
```{r}
log10(v)
```

### Environment

To see what is in current environment us *ls()* command:
```{r}
ls()
```

To remove items from environment, use *rm()* command:
```{r}
rm(x)
ls()
```

## Package Management

To see what is already present, use command:
```{r}
installed.packages()
```
```{r}
installed.packages("vegan", dependencies=TRUE)
```

## Project Management

1. Set up management structure (i.e., "data", "src [source]", "results", "doc"). Basic folders you should have when doing data analysis.
2. Avoiding redundancy of files
3. Make sure to use version control (i.e., Git)

## Getting Help
If you don't know what a command does, just place a question mark (?) infront of the command:
```{r}
?plot
```
You can also use the help command:
```{r}
help()
```
You can even use it with symbols:
```{r}
#? <-
```

```{r}
?"<-"
```
Can get vignette:
```{r}
vignette("FAQ-vegan")
```
To get citations:
```{r}
citation("vegan")
```
## Data and Their Formats

data.frame makes a spreadsheet (like in python)
```{r}
cats <- data.frame(coat = c("calico", "black", "tabby"), weight = c(2.1,5,3.2), likes_string = c(1,0,1))
```

```{r}
cats
```
```{r}
getwd()
```


To create a new column, use cbind:
```{r}
logweight <- log(cats$weight)
cbind(cats,logweight)
```
To print a string of text, use "paste" commmand:
```{r}
paste("My cat is ", cats$coat, ", and it weighs ", cats$weight, " kg.", sep = "")
```

### Data Types

```{r}
typeof(cats$coat)
```
```{r}
typeof(cats$weight)
```
 A  double represent a numver with decimal places
 
```{r}
typeof(cats$likes_string)
```
 
```{r}
typeof(3.14159)
```

```{r}
typeof(1i)
```

You can use "TRUE" & "FALSE"
```{r}
typeof(TRUE)
typeof(T)
typeof(FALSE)
typeof(F)
```

```{r}
typeof(cats)
```

```{r}
class(cats)
```

To open a file use:
```{r}
file.show()
```

To make 1=TRUE & 0=FALSE
```{r}
cats$likes_string <- as.logical(cats$likes_string)
typeof(cats$likes_string)
```
```{r}
cats$likes_string
```

```{r}
c("a", "b")
ab <-c("a","b")
ab
```

```{r}
c(ab, "c")
```

```{r}
c(ab, ab)
```
To get a range, just use a colon (:)
```{r}
1:10
```

You can also use seq(#):
```{r}
seq(10)
```

```{r}
z <- seq(10)
head(z, n=3)
```
```{r}
length(z)
class(z)
typeof(z)
```
```{r}
seq(1,100, by=5)
```

Gives you 1 to 100 in intervals of 5

```{r}
seq(70,100, by=5)
```

### Data Frames

```{r}
cats <- cbind(cats,logweight)
cats
```

```{r}
str(cats$coat)
```

```{r}
str(cats$coat)
```

```{r}
coats <- "tabby", "tortoiseshell" "tortoiseshell", "black", "tabby"
coats
```

```{r}
factor("coats")
```

```{r}
categories <- factor(coats)
class(coats)
class(categories)
```

### Lists

```{r}
list_example <- list(title="Numbers", numbers=1:10, data=TRUE)
list_example
```
```{r}
another_list <- list(1,"a", TRUE, 1+1i)
another_list
```
```{r}
typeof(list_example)
class(list_example)

typeof(another_list)
class(another_list)

typeof(cats)
class(cats)
```

To turrn lists -> data.frame
```{r}
data.frame(list_example)
data.frame(another_list)
```
To subset lists, # after comma means look at colomuns, # before means look at row:
```{r}
cats
```

```{r}
cats[,3]
cats[3,]
```

```{r}
cats[2:3,c(1,3)]
```

### Matrices

Matrix: made for math, all numbers

Data.frame/spreadsheet: can be quantitative or qualitative

```{r}
matrix_example <- matrix(0,ncol=5, nrow=3)
matrix_example
```

```{r}
class(matrix_example)
```

```{r}
typeof(matrix_example)
```

```{r}
str(matrix_example)
```

```{r}
dim(matrix_example)
```

```{r}
ncol(matrix_example)
```

```{r}
nrow(matrix_example)
```

To turn a matrix into a spreadsheet
```{r}
class(data.frame(matrix_example))
```

To save as a data.frame
```{r}
df_example <- data.frame(matrix_example)
df_example
```

### Subsetting
Works with dataframes & matrices

```{r}
p <- c(2.3, 6.9, 4.0, 23, 1)
p
```

TO apply names to vector use:
```{r}
names(p) <- c('a', 'b', 'c', 'd', 'e')
p
```

```{r}
p[1]
```

```{r}
p[2:4]
```

```{r}
p[c(1,5)]
```

```{r}
p[c(1,1,1,3,4,5)]
```

To remove columns, use a (-)
```{r}
p[-3]
```

```{r}
p[c(-1,-5)]
```

```{r}
p[-(2:4)]
```

```{r}
p[c('a','c')]
```

To say not equal to, use !=
```{r}
p[names(p) !='c']
```

### Factors

```{r}
f <- factor(c('a', 'b', 'c','d', 'e'))
f
```

To do absolutely is equal to, use double ='s
```{r}
f[f == 'a']
```

```{r}
f[1:3]
```

To see if the factor contains some option, use %in%
```{r}
f[f %in% c('b','c')]
```

```{r}
f[-3]
```

```{r}
f2 <- factor(c('a','a','b','c','c'))
f2
```

```{r}
f2[f2 == 'a']
```

```{r}
f2 [f2 %in% c('a','c')]
```

### Matrices Resumed
Setting the seed will make sure you get the same result everytime.
```{r}
set.seed(65)
m <- matrix(rnorm(6*4), ncol=4, nrow=6)
m
```

## Slicing Matrices
For specific rows
```{r}
m[3:4, c(3,1)]
```

For specific columns
```{r}
m[,c(3,4)]
```

### Lists

```{r}
xlist <- list(a="BIOL48006220", b=seq(1,10, by = 0.5), data="Grades")
xlist
```

by = 0.5 is step size/increment

```{r}
xlist[1:2]
```


```{r}
xlist['a']
```
You can also subslice by using [[]] to represent just the value not the object
```{r}
xlist[['a']]
```

```{r}
xlist['b']
```

```{r}
xlist[['b']]
```

You can use a $ to represent what ever the values are:
```{r}
xlist$b
```

### Date Frames
```{r}
gp <- read.csv('/Users/maggieshostak/Desktop/Practical\ Computing/Class\ Examples/PracticalComputing_2022/data/forest_area_sq_km.csv')
head(gp, n=10L)
```
```{r}
head(gp[3], n=10L)
```
To determine how many rows
```{r}
nrow(gp)
```

```{r}
head(gp["country"])
```

```{r}
head(gp[["country"]], 10L)
```

```{r}
gp$X1997
```

To just look at rows 1-3 & columns 2-5
```{r}
gp[1:3, 2:5]
```
To just look at columns 1 & 3 & 4 & 5
```{r}
gp[c(1,3), c(2,5)]
```
```{r}
gp[ which(gp$X1989 <= 100 & gp$X2019 >= 100),]
```

### Conditionals & Flow
To indent we use { then press enter to make conditional statement:
```{r}
n <- 10

if (n<10) {
  print("n is less than 10")
} else if (n>10) {
  print("n is more than 10")
} else {
  print("n is equal to 10")
}
```

```{r}
for (n in seq(1,20)) {
  if (n<10) {
    print("n is less than 10")
  } else if (n>10) {
    print("n is more than 10")
  } else {
    print("n is equal to 10")
  }
}
```

Paste is like the cat command:
```{r}
g <- 0

while (g <=10) {
  print(paste(g, "is less than or equal to 10"))
  g <- g+1
}
```

### Plotting & Figures

```{r}
#installed.packages('ggplot2')
```

```{r}
library(ggplot2)
```

```{r}
gp <- read.csv('/Users/maggieshostak/Desktop/Practical\ Computing/Class\ Examples/PracticalComputing_2022/data/gapminder_all.csv')

head(gp)
```
```{r}
ggplot(data=gp, mapping=aes(x=gdpPercap_1952, y=pop_1952)) + geom_point()
```

```{r}
ggplot(data=gp, mapping=aes(x=gdpPercap_2002, y=pop_2002)) + geom_point()
```

```{r}
gapminder <- read.csv("https://raw.githubusercontent.com/swcarpentry/r-novice-gapminder/gh-pages/_episodes_rmd/data/gapminder_data.csv")
head(gapminder)
```
```{r}
ggplot(data=gapminder, mapping=aes(x=gdpPercap, y=lifeExp)) + geom_point()
```

```{r}
ggplot(data=gapminder, mapping=aes(x=year, y=lifeExp, by=country, color=continent)) + geom_line()
```


```{r}
ggplot(data=gapminder, mapping=aes(x=year, y=lifeExp, by=country)) + geom_line(mapping=aes(color=continent)) + geom_point()
```

To transfer an exponential model, use the log10:
```{r}
ggplot(data=gapminder, mapping=aes(x=gdpPercap, y=lifeExp)) + geom_point() + scale_x_log10()
```
```{r}
ggplot(data=gapminder, mapping=aes(x=gdpPercap, y=lifeExp)) + geom_point(alpha=0.5) + scale_x_log10()
```

```{r}
ggplot(data=gapminder, mapping=aes(x=gdpPercap, y=lifeExp)) + geom_point(alpha=0.1) + scale_x_log10()
```

```{r}
ggplot(data=gapminder, mapping=aes(x=gdpPercap, y=lifeExp)) + geom_point(alpha=0.25, color="purple", size=0.9, pch=15) + scale_x_log10() + geom_smooth(method=lm, color="gold", size=1.5)
```


```{r}
Africas <- gapminder[gapminder$continent == "Africa", ]
head(Africas)

```

Facet_wrap: tells you how you want to plot them independetly 
```{r}
ggplot(data=Africas, mapping=aes(x=year, y=lifeExp)) +
  geom_line() +
  facet_wrap(~ country)
```

```{r}
ggplot(data=Africas, mapping=aes(x=year, y=lifeExp)) +
  geom_line() +
  facet_wrap(~ country) +
  theme(axis.text.x = element_text(angle=90))
```

```{r}
ggplot(data=Africas, mapping=aes(x=year, y=lifeExp)) +
  geom_line(color="red") +
  facet_wrap(~ country) +
  theme(axis.text.x = element_text(angle=90)) +
  labs(
    x="Year",
    Y="lifeExp",
    Title="Life Exoectency Over Time in African Countries",
  )
```

How to save a graph to make an output file:
```{r}
AfricanLifeExpectancy <- ggplot(data=Africas, mapping=aes(x=year, y=lifeExp)) +
  geom_line(color="red") +
  facet_wrap(~ country) +
  theme(axis.text.x = element_text(angle=90)) +
  labs(
    x="Year",
    Y="lifeExp",
    Title="Life Expectency Over Time in African Countries",
  )
```

```{r}
ggsave(filename="data/AfricanLifeExpectancy.png", plot=AfricanLifeExpectancy, width=24, height=40, dpi=300, units="cm")
```


```{r}
pdf(file="results/AfricanLifeExp.pdf", width=24, height=40)
plot(AfricanLifeExpectancy)
dev.off()
```


```{r}
write.table(gapminder, file="data/gapminder_web.csv", sep=",")
```

```{r}
write.csv(Africas, file="data/gapmminder_web_africas.csv")
```

### Fancy Plots

```{r}
#install.packages(c("ggridges", "viridis", "hrbrthemes", dependencies=T))
```
```{r}
library(ggridges)
library(ggplot2)
library(viridis)
library(hrbrthemes)
```
```{r}
hrbrthemes::import_roboto_condensed()
```

..x.. makes it a gradient fill & smooth

```{r}
ggplot(lincoln_weather, aes(x=`Mean Temperature[F]`, y= `Month`, fill=..x..)) + geom_density_ridges_gradient(scale = 3, rel_min_height = 0.01) + scale_fill_viridis(name="temp. [F]", option = "A") + theme_ipsum() +
  theme(
    legend.position="none",
    panel.spacing = unit(0.1, "lines"),
    strip.text.x = element_text(size=8))
```


Themes dictate fonts

Taking family and year described, use bin to make a hard/bar plot


```{r}
install.packages(c("ggstatsplot", "palmerpenguins", dependencies=T))
```

```{r}
library(tidyverse)
library(ggstatsplot)
```

```{r}
data("penguins", package = "palmerpenguins")
penguins
```

```{r}
penguins2 <-  drop_na(penguins)
penguins2
```
```{r}
plt <- ggbetweenstats(
  data = penguins,
  x=species,
  y=bill length)
plt
```

```{r}
gapminder2 <- drop_na(gapminder)
```

```{r}
boxplot(gapminder2$lifeExp ~ gapminder2$continent)
```
Box plots don't show distribution, instead use a violin plot
```{r}
install.packages("vioplot", dependencies = T)
```
```{r}
library(vioplot)
```

```{r}
with(gapminder2, vioplot(
  lifeExp~continent, col="orange"
))
```

```{r}
plt <- ggbetweenstats()
```

To save/export graph
```{r}
ggsave(
  flename = "insert name",
  plot = plt
  width  = 8
  height = 8
  device = "png"
)
```
 You can then load the stuff in InkScape to adjust the visual aesthetics

## PCA Plots
```{r}
penguins2
```
For principle components, you need a matrix
```{r}
penguins_matrix <- with(penguins2, cbind(bill_length_mm, bill_depth_mm, flipper_length_mm, body_mass_g))
penguins_matrix
```

```{r}
penguin_pca <- princomp(penguins_matrix, cor = TRUE)
summary(penguin_pca)
```
Component 1 represents # of dimensions you have (x-axis, y-axis, z-axis & 4th-axes) and it rotates/interactions it based on categories [this will change the axes]

Individual Loadings
```{r}
loadings(penguin_pca)
```

```{r}
biplot(penguin_pca, xlab=penguins2[,2])
```


```{r}
levels(penguins2$species)
```

To get PCA scores
```{r}
penguin_pca$scores
```

*ADD LESSON STUFF FROM LAST CLASS*

## Statistics

### Additional Ways of Importing, Reading, and Manipulating Data


Hard method:
```{r}
rand <- c(12, 54, 98, 65, 38)
rand
```

To get cumulative sum:
```{r}
sum(rand)
```

```{r}
length(rand)
```

To get the mean of your data:
```{r}
avg.rand <- (sum(rand)/length(rand))
avg.rand
```
Another way to get the average:

```{r}
mean(rand)
```

To sort:
```{r}
sort(rand)
```

```{r}
min(rand)
```

```{r}
max(rand)
```

```{r}
cumsum(rand)
```

To get differences:
```{r}
diff(rand)
```

Slicing/Indexing #'s out:
```{r}
rand[2]
```

Transforming #'s: adding, multiplying, etc

Importing Data, Most Useful: Take a list of numbers, don't need to add comma's and just paste in data. Press 'enter' twice to finish adding data
```{r}
peds <- scan()
peds
```

### Analyses

#### Univariate Statistics

##### 1. Categotical Data
######  a. Barplots

```{r}
beer <- c(3, 4, 1, 1, 3, 4, 3, 3, 1, 3, 2, 1, 2, 1, 2, 3, 2, 3, 1, 1, 1, 1, 4, 3, 1)
length(beer)
```
You cannot use "barplot(beer)" command right away. It will just show you every # in its own column

```{r}
table(beer)
```

```{r}
barplot(table(beer))
```
This is just for counts/frequency:
```{r}
barplot(table(beer), xlab="Beer", ylab="Frequency")
```
For proportion:
```{r}
barplot(table(beer)/length(beer), xlab="Beer", ylab="Proportion")
```
###### b. Pie Charts
```{r}
pie(table(beer), main="Beer Preference By Students")
```


##### 2. Numerical Data

###### a. Stem-and-Leaf Plots
```{r}
stem(peds)
```

###### b. Strip Chart
```{r}
stripchart(peds, method="stack")
```

##### 3. Measures of Center

###### a. Mean
```{r}
mean(peds)
```

Using Columns in Data frame:
```{r}
mean(gapminder2$lifeExp)
```

###### b. Median
```{r}
median(peds)
```

```{r}
median(gapminder2$lifeExp)
```

Must know exact column headers using the "with" command
```{r}
with(gapminder2, median(lifeExp))
```

###### c. Mode

Frequency of measurement occurring:
```{r}
which(table(peds) == max(table(peds)))
```

##### 4. Variation/Spread

###### a. Range
```{r}
range(peds)
```

Will give you a summary of the range:
```{r}
diff(range(peds))
```

###### b. Variance
```{r}
var(peds)
```

Standard Deviation: sqrt of variance
```{r}
sd(peds)
```

###### c. Inter-quartile Range (IQR)
```{r}
IQR(peds)
```

###### d. Z-Scores
The number of standard deviations away from the mean
```{r}
scale(peds)
```

###### e. Summaries
```{r}
summary(peds)
```

##### 5. Plotting

###### a. Histogram
```{r}
hist(peds)
```
Modify # of breaks:
```{r}
hist(peds, breaks=2)
```


```{r}
hist(peds, breaks="scott")
```

```{r}
hist(peds, breaks="scott", prob=TRUE) #To look at the densities
```

```{r}
hist(peds, breaks="scott", prob=TRUE)
lines(density(peds))
```

```{r}
plot(density(peds))
```

##### b. Boxplots

```{r}
boxplot(peds)
```

#### Bivariate & Multivariate Statistics

##### 1. Plotting & Regression

###### a. Boxplotting
```{r}
spid.gen <- read.csv("/Users/maggieshostak/Downloads/spider_genitalia.csv", header = TRUE)
spid.gen
```
```{r}
boxplot(spid.gen) # This is a spreadsheet so it won't work
```
```{r}
boxplot(spid.gen$left.bulb ~ spid.gen$habitat)
```
```{r}
boxplot(spid.gen$left.bulb/spid.gen$carapace.length ~ spid.gen$habitat)
```

###### b. Scatterplots

```{r}
plot(spid.gen$left.bulb ~ spid.gen$right.bulb)
```

Changing plot characters using pch
```{r}
plot(spid.gen$left.bulb ~ spid.gen$right.bulb, pch = as.character(spid.gen$habitat))
```

###### c. Linear Regression

To use a linear model, define general regression variable using lm():
```{r}
gen.reg <- lm(spid.gen$left.bulb ~ spid.gen$right.bulb)
gen.reg
```

Using summary(gen.reg) will result in an ANOVA test:
```{r}
summary(gen.reg)
```

Using abline will give you your linear regression line into your plot:
```{r}
plot(spid.gen$left.bulb ~ spid.gen$right.bulb, pch = as.character(spid.gen$habitat))
abline(gen.reg)
```

###### d. Correlation Coefficient & Spearman Rank Correlation

Cor.gen will give you your R-value, to get R^2, use cor.gen^2:
```{r}
cor.gen <- with(spid.gen, cor(left.bulb, right.bulb))
cor.gen
cor.gen^2
```

```{r}
spearman.cor.gen <- with(spid.gen, cor(left.bulb, right.bulb, method="spearman"))
spearman.cor.gen^2
```

###### e. Residuals

Residuals are the difference between a value and the line of best fit (LOBF)
```{r}
residuals(gen.reg)
```

###### f. Transformations

```{r}
plot(spid.gen$left.bulb^2~spid.gen$right.bulb^2)
```

```{r}
plot(log10(spid.gen$left.bulb)~spid.gen$right.bulb)
```
```{r}
log.left.bulb <- log10(spid.gen$left.bulb)
```


##### 2. Comparing Descrete Treatment Effects

###### a. Chi-Squared Test

```{r}
obs <- c(4,15,6,15,18,2)
exp <- c(0.16,0.17,0.16,0.17,0.17,0.17)
chisq.test(obs, p=exp)
```

```{r}
obs_weighted <- c(4,15,6,15,18,2)
obs_fair <- c(10,10,10,10,10,10)
exp <- c(0.16,0.17,0.16,0.17,0.17,0.17)
```

This will be significant:
```{r}
chisq.test(obs_weighted, p=exp)
```

This is not significant since p=value is 1:
```{r}
chisq.test(obs_fair, p=exp)
```

###### b. T-test

Null hypothesis (H0):  true mean is equal to zero, but you can set true mean to other values with "mu="

1 Sample T-Test: Student T-Test (2-Tail Test)
```{r}
t.test(spid.gen$carapace.length)
```

```{r}
mean(spid.gen$carapace.length)
```

```{r}
t.test(spid.gen$carapace.length, mu=29)
```

2 Sample T-Test:
```{r}
habitat.t2 <- t.test(spid.gen$carapace.length~spid.gen$habitat)
habitat.t2
```
```{r}
habitat.t2 <- t.test(spid.gen$left.bulb~spid.gen$habitat)
habitat.t2
```

1 Sample Test: Is one less than the other? (1-Tailed)
```{r}
habitat.tless <- t.test(spid.gen$left.bulb, alternative = "less")
habitat.tless
```

Conclusion: B is not less than A

1 Sample Test: Is one greater than the other? (1-Tailed)
```{r}
habitat.tgreater <- t.test(spid.gen$left.bulb, alternative = "greater")
habitat.tgreater
```


###### c. Analysis Of Variance (ANOVA)


```{r}
gen.lm <- lm(spid.gen$left.bulb~spid.gen$habitat)
gen.lm
```

```{r}
summary(gen.lm)
```

```{r}
anova(gen.lm)
```

```{r}
gen.anova <- aov(spid.gen$left.bulb~spid.gen$habitat)
gen.anova
```

```{r}
summary(gen.anova)
```

Note: You get the same output

```{r}
gapminder2.lifeexp.continent.anova <- aov(gapminder2$lifeExp~gapminder2$continent)
summary(gapminder2.lifeexp.continent.anova)
```

Performing a Post Hoc Test: Tukey Test
```{r}
gapminder2.tukey.two.way <- TukeyHSD(gapminder2.lifeexp.continent.anova)
gapminder2.tukey.two.way
```

###### d. Analysis of Covariance (ANCOVA)

Supplying to model other factors that might explain the differences
```{r}
boxplot(spid.gen$left.bulb~spid.gen$habitat)
```
Use a covariate by adding *factor_you_want_to_control
```{r}
gen.ancova <- lm(spid.gen$left.bulb~spid.gen$habitat*spid.gen$carapace.length)
summary(gen.ancova)
```

```{r}
gapminder2.lifeexp.continent_GDP.ancova <- aov(gapminder2$lifeExp~gapminder2$continent+gapminder2$gdpPercap)
summary(gapminder2.lifeexp.continent_GDP.ancova)
```

```{r}
install.packages("multcomp")
```
```{r}
library(multcomp)
```

```{r}
#posthoc.gapminder2.ancova <- glht(gapminder2.lifeexp.continent_GDP.ancova, linfct=mcp(technique="Tukey")) (isn't working)
```

##### 3. Principle Component Analysis

```{r}
sp.matrix <- with(spid.gen, cbind(left.bulb, right.bulb, carapace.length, leg4.length))
sp.matrix
```
```{r}
sp.pca <- princomp(sp.matrix, cor=TRUE)
summary(sp.pca)
```

```{r}
loadings(sp.pca)
```
```{r}
biplot(sp.pca)
```
```{r}
install.packages("ggfortify", dependencies = TRUE)
```

```{r}
sp.pca$scores
```


```{r}
library(ggfortify)
```

```{r}
sp.pca.plot <- autoplot(sp.pca,
                        data=spid.gen,
                        colour="habitat")
sp.pca.plot
```
# Plot Cheatsheet
```{r}
plot(1:25, rep(0.25,25), pch=1:25, col=1:25, ylim=c(0,6), cex=2, ylab="Line types (lty) 1 to 6", xlab="Plotting character (pch) 1 to 25 and colours (col) 1 to 8", main="Line types (lty), plotting characters (pch),\nand colors (col) for plot and xyplot", lab=c(25,7,2))

points(1:8, rep(0.5,8), pch=20, col=1:8, cex=4)

abline(h=1:6, lty=1:6, lwd=5, col=1:8)
```

# Looping and Conditionals

## A. If-Then Statements
```{r}
x <- 5
if(x > 0){
  print("Positive #")}
```

```{r}
x <- -5
if(x > 0){
  print("Positive #")
} else if (x < 0) {
  print("Negative #")
} else
  print("Zero")
```

%% Represents division, and == means no remainder "if its true", "if its odd"

```{r}
a <- c(5,7,2,9)
ifelse(a %% 2 == 0, "even", "odd")
```

## B. For Loops

For each of these values in Z, divide them by 2, if they don't have a remainder, it will tell you how many even numbers
```{r}
z <- c(2,5,3,9,8,11,6)
count <- 0

for(val in z) {
  if(val %% 2 == 0) count = count + 1
}
  print(count)
```

## C. While Statement

```{r}
i <- 1
while (i < 5) {
  print(i)
  i = i +1
}
```

## D. Interruptions

Breaks the loop
```{r}
x <- 1:5
for (val in x){
  if (val == 3){
    break
  }
  print(val)
}
```

If print(val) is placed before the break, it will print the value 3, then break the loop
```{r}
x <- 1:5
for (val in x){
  if (val == 3){
    print(val)
    break
  }
  #print(val)
}
```

```{r}
x <- 1:5
for (val in x){
  print(val)
  if (val == 3){
    #print(val)
    break
  }
  #print(val)
}
```

If the value is equal to 3, it will skip that value and move onto the next one
```{r}
for (val in x){
  if (val == 3) {
    next
  }
  print(val)
}
```

```{r}
x <- 1
repeat{
  print(x)
  x = x+1
  if (x == 20) {
    break
  }
}
```
# Randomization & Dataset Management (short)

## A. Dataset Management

```{r}
matrix_B <- matrix(
  c(2,4,3,1,5,7),
  nrow=3,
  ncol=2
)

matrix_B
```

Transforming Data
```{r}
t(matrix_B)
```

```{r}
matrix_C <- matrix(
  c(7,4,2),
  nrow=3,
  ncol=1
)

matrix_C
```
Putting the Matrices/Data.frame together
```{r}
matrix_BC <- cbind(matrix_B, matrix_C)
matrix_BC
```

Deconstructing the Matrices
```{r}
c(matrix_BC)
```

## B. Randomizations
Each tiime you run the script, you will get different numbers

rnorm(# samples, average, variance as standard deviation)
sample(what you want to sample, size of sample, replace = FALSE, prob = NULL)

```{r}
ndist <- rnorm(100, 50, 20)
ndist 
```
```{r}
hist(ndist)
```


```{r}
sample(ndist, 10, replace = FALSE, prob = NULL)
```

### Sampling With & Without Replacement
```{r}
test <- 1:100
test
```

No repeats:
```{r}
sort(sample(test, 50, replace = FALSE, prob = NULL))
```

Now you can have repeats:
```{r}
sort(sample(test, 50, replace = TRUE, prob = NULL))
```

